diff --git a/anvio/__init__.py b/anvio/__init__.py
index 4e9e19503..8ec79fcab 100644
--- a/anvio/__init__.py
+++ b/anvio/__init__.py
@@ -181,6 +181,14 @@ def TABULATE(table, header, numalign="right", max_width=0):
                      "You can provide these names as a comma-separated list of names, or you can put them in a file, "
                      "where you have a single genome name in each line, and provide the file path."}
                 ),
+    'genomes-reverse': (
+            ['-R', '--genome-reverse'],
+            {'metavar': "GENOME_NAMES",
+             'required': False,
+             'help': "Genome names to 'reverse'. You can use this parameter to choose the genomes whose synteny you want to reverse. "
+                     "You can provide these names as a comma-separated list of names, or you can put them in a file, "
+                     "where you have a single genome name in each line, and provide the file path."}
+                ),
     'blank-profile': (
             ['--blank-profile'],
             {'default': False,
@@ -2115,6 +2123,74 @@ def TABULATE(table, header, numalign="right", max_width=0):
              'type': str,
              'help': "Directory path for output files"}
                 ),
+     # start of anvi-pan-graph related input and output variables:
+    'testing-yaml': (
+            ['--testing-yaml'],
+            {'metavar': 'YAML',
+             'type': str,
+             'help': "A yaml file containing raw gene cluster order for testing the anvi'o pan graph."}
+                ),
+    'gene-additional-data': (
+            ['--gene-additional-data'],
+            {'metavar': 'CSV',
+             'type': str,
+             'help': "A CSV file containing at least one column with values per genome, contig and genecall column."}
+                ),
+    'gc-additional-data': (
+            ['--gc-additional-data'],
+            {'metavar': 'CSV',
+             'type': str,
+             'help': "A CSV file containing at least one column with values per genome, contig and gc column."}
+                ),
+     'output-pan-graph-json': (
+            ['-o', '--output-pan-graph-json'],
+            {'metavar': 'FILE_PATH',
+             'type': str,
+             'help': "File path to store the temporary pan-graph-json file."}
+                ),
+     'output-graphml': (
+            ['--output-graphml'],
+            {'metavar': 'FILE_PATH',
+             'type': str,
+             'help': "File path to store the final graph file."}
+                ),
+     'output-raw-gc-additional-data': (
+            ['--output-raw-gc-additional-data'],
+            {'metavar': 'FILE_PATH',
+             'type': str,
+             'help': "File path to create and store a raw gc additional data table for testing or join purposes."}
+                ),
+     'output-raw-gene-additional-data': (
+            ['--output-raw-gene-additional-data'],
+            {'metavar': 'FILE_PATH',
+             'type': str,
+             'help': "File path to create and store a raw gc additional data table for testing or join purposes."}
+                ),
+     'output-testing-yaml': (
+            ['--output-testing-yaml'],
+            {'metavar': 'FILE_PATH',
+             'type': str,
+             'help': "File path to create and store a testing yaml for a existing pangenome."}
+                ),
+     'output-dir-summary': (
+            ['--output-dir-summary'],
+            {'metavar': 'DIR_PATH',
+             'type': str,
+             'help': "File path to store a CSV file containing values describing the pan-graph for downstream analysis."}
+                ),
+     'output-dir-graphics': (
+            ['--output-dir-graphics'],
+            {'metavar': 'DIR_PATH',
+             'type': str,
+             'help': "File path to store the hierarchical clusterings for the paralog splitting."}
+                ),
+     'pan-graph-json': (
+            ['-i', '--pan-graph-json'],
+            {'metavar': 'JSON',
+             'type': str,
+             'help': "A JSON formatted anvi'o pan graph, which is typically generated by `anvi-pan-graph`."}
+                ),
+    # end of pan-graph related variables
     'output-file': (
             ['-o', '--output-file'],
             {'metavar': 'FILE_PATH',
@@ -3701,6 +3777,7 @@ def set_version():
            anvio_codename, \
            t.contigs_db_version, \
            t.pan_db_version, \
+           t.pangraph_json_version, \
            t.profile_db_version, \
            t.genes_db_version, \
            t.auxiliary_data_version, \
@@ -3717,6 +3794,7 @@ def get_version_tuples():
             ("Genes DB version", __genes__version__),
             ("Auxiliary data storage version", __auxiliary_data_version__),
             ("Pan DB version", __pan__version__),
+            ("Pangraph JSON version", __pangraph__version__),
             ("Genome data storage version", __genomes_storage_version__),
             ("Structure DB version", __structure__version__),
             ("KEGG Modules DB version", __kegg_modules_version__),
@@ -3729,6 +3807,7 @@ def print_version():
     run.info("Profile database", __profile__version__)
     run.info("Contigs database", __contigs__version__)
     run.info("Pan database", __pan__version__)
+    run.info("Pangraph JSON", __pangraph__version__)
     run.info("Genome data storage", __genomes_storage_version__)
     run.info("Auxiliary data storage", __auxiliary_data_version__)
     run.info("Structure database", __structure__version__)
@@ -3740,6 +3819,7 @@ def print_version():
 __codename__, \
 __contigs__version__, \
 __pan__version__, \
+__pangraph__version__, \
 __profile__version__, \
 __genes__version__, \
 __auxiliary_data_version__, \
diff --git a/anvio/bottleroutes.py b/anvio/bottleroutes.py
index ef6e8dbcb..30bb53bd4 100644
--- a/anvio/bottleroutes.py
+++ b/anvio/bottleroutes.py
@@ -21,6 +21,7 @@
 import argparse
 import datetime
 import importlib
+import networkx as nx
 
 from hashlib import md5
 from ete3 import Tree
@@ -38,6 +39,7 @@
 
 import anvio
 import anvio.dbops as dbops
+import anvio.panops as panops
 import anvio.utils as utils
 import anvio.drivers as drivers
 import anvio.terminal as terminal
@@ -197,7 +199,12 @@ def register_routes(self):
         self.route('/data/get_gene_info/<gene_callers_id>',    callback=self.get_gene_info)
         self.route('/data/get_metabolism',                     callback=self.get_metabolism)
         self.route('/data/get_scale_bar',                      callback=self.get_scale_bar, method='POST')
-
+        self.route('/pangraph/settings',                       callback=self.get_pangraph_settings, method="POST")
+        self.route('/pangraph/get_json',                       callback=self.get_pangraph_json_data, method="POST")
+        self.route('/pangraph/alignment',                      callback=self.get_pangraph_gc_alignment, method="POST")
+        self.route('/pangraph/analyse',                        callback=self.get_pangraph_bin_summary, method="POST")
+        self.route('/pangraph/function',                       callback=self.get_pangraph_gc_function, method="POST")
+        self.route('/pangraph/filter',                         callback=self.get_pangraph_passed_gene_clusters, method="POST")
 
     def run_application(self, ip, port):
         # check for the wsgi module bottle will use.
@@ -266,6 +273,8 @@ def redirect_to_app(self):
             homepage = 'structure.html'
         elif self.interactive.mode == 'metabolism':
             homepage = 'metabolism.html'
+        elif self.interactive.mode == 'pangraph':
+            homepage = 'pangraph.html'
         elif self.interactive.mode == 'inspect':
             redirect('/app/charts.html?id=%s&show_snvs=true&rand=%s' % (self.interactive.inspect_split_name, self.random_hash(8)))
 
@@ -1069,7 +1078,7 @@ def gen_summary(self, collection_name):
 
         path = "summary/%s/index.html" % (collection_name)
         return json.dumps({'path': path})
-        
+
 
     def send_summary_static(self, collection_name, filename):
         if self.interactive.mode == 'pan':
@@ -1534,7 +1543,7 @@ def get_functions_for_gene_clusters(self):
                 message = (f"At least one of the gene clusters in your list (e.g., {gene_cluster_name}) is missing in "
                            f"the functions summary dict :/")
                 return json.dumps({'status': 1, 'message': message})
-                
+
             d[gene_cluster_name] = self.interactive.gene_clusters_functions_summary_dict[gene_cluster_name]
 
         return json.dumps({'functions': d, 'sources': list(self.interactive.gene_clusters_function_sources)})
@@ -1551,4 +1560,133 @@ def get_scale_bar(self):
             message = str(e.clear_text()) if hasattr(e, 'clear_text') else str(e)
             return json.dumps({'status': 1, 'message': message})
             
-        return json.dumps({'scale_bar_value': total_branch_length})
\ No newline at end of file
+        return json.dumps({'scale_bar_value': total_branch_length})
+
+    def get_pangraph_json_data(self):
+
+        return self.interactive.get_pangraph_json()
+    
+
+    def get_pangraph_bin_summary(self):
+
+        payload = request.json
+        selection = payload['selection']
+        result = {}
+
+        self.interactive.init_gene_clusters()
+        self.interactive.init_gene_clusters_functions_summary_dict()
+
+        bin_functions = {}
+        all_functions = []
+
+        for bin in list(payload.keys())[1:]:
+            
+            bin_functions[bin] = []
+            gene_cluster_list = payload[bin]
+            for gene_cluster_name in gene_cluster_list:
+                function = self.interactive.gene_clusters_functions_summary_dict[gene_cluster_name][selection]['function']
+                
+                bin_functions[bin].append(function)
+                all_functions.append(function)
+                
+        for function in all_functions:
+            result[function] = {}
+            for bin in bin_functions.keys():
+                if function in bin_functions[bin]:
+                    result[function][bin] = 1
+                else:
+                    result[function][bin] = 0
+
+        return json.dumps(result)
+
+    def get_pangraph_settings(self):
+
+        payload = request.json
+        max_edge_length_filter = payload['maxlength']
+        gene_cluster_grouping_threshold = payload['condtr']
+        groupcompress = payload['groupcompress']
+        ungrouping_area = payload['ungroup']
+        print(ungrouping_area)
+
+        args = argparse.Namespace(
+            pan_graph_json=self.interactive.pan_graph_json_path,
+            output_pan_graph_json=self.interactive.pan_graph_json_path,
+            max_edge_length_filter=max_edge_length_filter,
+            gene_cluster_grouping_threshold=gene_cluster_grouping_threshold,
+            gene_cluster_grouping_compression=groupcompress,
+            ungrouping_area = ungrouping_area
+            )
+
+        Pangraph = panops.Pangraph(args)
+
+        Pangraph.load_graph_from_json_file()
+        Pangraph.run_synteny_layout_algorithm()
+        Pangraph.update_json_dict()
+        Pangraph.store_network()
+
+        return({'status': 0})
+
+    def get_pangraph_gc_alignment(self):
+
+        payload = request.json
+        result = {}
+
+        for genome in payload.keys():
+            genecall, contig, direction, name = payload[genome]
+            gene_cluster_alignment_dict = self.interactive.get_sequences_for_gene_clusters(gene_cluster_names=set([name]), skip_alignments=False, report_DNA_sequences=False)[name]
+            sequence = gene_cluster_alignment_dict[genome][int(genecall)]
+
+            result[genome] = [genecall, contig, direction, sequence]
+
+        return(result)
+    
+    def get_pangraph_gc_function(self):
+
+        payload = request.json
+        result = {}
+
+        self.interactive.init_gene_clusters()
+        self.interactive.init_gene_clusters_functions_summary_dict()
+
+        gene_cluster_name = payload['genecluster']
+
+        for selection in self.interactive.gene_clusters_functions_summary_dict[gene_cluster_name].keys():
+            result[selection] = self.interactive.gene_clusters_functions_summary_dict[gene_cluster_name][selection]
+        return json.dumps(result)
+    
+    def get_pangraph_passed_gene_clusters(self):
+
+        payload = request.json
+        result = {'gene_clusters': []}
+
+        self.interactive.init_gene_clusters()
+        self.interactive.init_gene_clusters_functions_summary_dict()
+
+        functions_dict = self.interactive.gene_clusters_functions_summary_dict
+
+        for gene_cluster in functions_dict.keys():
+            for selection in payload.keys():
+                if selection in functions_dict[gene_cluster].keys():
+                    for search in payload[selection]:
+                        value = functions_dict[gene_cluster][selection]
+
+                        accession = value['accession']
+                        func = value['function']
+
+                        if not accession or not func:
+                            accession = ''
+                            func = ''
+
+                        if search == '':
+
+                            print(search, accession, func)
+                            if search == accession or search == func:
+                                if gene_cluster not in result['gene_clusters']:
+                                    result['gene_clusters'] += [gene_cluster]
+
+                        else:
+                            if search.lower() in accession.lower() or search.lower() in func.lower():
+                                if gene_cluster not in result['gene_clusters']:
+                                    result['gene_clusters'] += [gene_cluster]
+
+        return json.dumps(result)
\ No newline at end of file
diff --git a/anvio/clustering.py b/anvio/clustering.py
index d224d1640..c5430b851 100644
--- a/anvio/clustering.py
+++ b/anvio/clustering.py
@@ -103,6 +103,23 @@ def get_newick_tree_data_for_dict(d, transpose=False, linkage=constants.linkage_
     return newick
 
 
+def get_newick(node, parent_dist, leaf_names, newick=''):
+    """
+    Modified from the solution at https://stackoverflow.com/questions/28222179/save-dendrogram-to-newick-format
+    """
+    if node.is_leaf():
+        return "%s:%.2f%s" % (leaf_names[node.id], parent_dist - node.dist, newick)
+    else:
+        if len(newick) > 0:
+            newick = "):%.2f%s" % (parent_dist - node.dist, newick)
+        else:
+            newick = ");"
+        newick = get_newick(node.get_left(), node.dist, leaf_names, newick=newick)
+        newick = get_newick(node.get_right(), node.dist, leaf_names, newick=",%s" % (newick))
+        newick = "(%s" % (newick)
+        return newick
+
+
 def get_vectors_for_vectors_with_missing_data(vectors):
     """Get a distance matrix for vectors with missing data.
 
diff --git a/anvio/data/interactive/css/pangraph.css b/anvio/data/interactive/css/pangraph.css
new file mode 100644
index 000000000..fd0b7e590
--- /dev/null
+++ b/anvio/data/interactive/css/pangraph.css
@@ -0,0 +1,244 @@
+@import url('variable.css');
+@import url('main.css');
+
+.gene-sequence{
+  font-family: monospace !important;
+}
+
+#svgbox {
+    position: relative;
+    height: 100vh;
+    width: 100vw;
+  }
+  
+  .offcanvas-btn {
+      visibility: visible;
+  }
+  
+  .offcanvas-btn span:last-child,
+  .offcanvas.show .offcanvas-btn span:first-child {
+    display: none;
+  }
+  
+  .offcanvas.show .offcanvas-btn span:last-child {
+    display: inline;
+  }
+  
+  h5 {
+    border-bottom: 1px solid #ccc; /* This is the line replacing the hr*/
+    margin-bottom: 10px; /* This is the space below the line */
+    margin-top: 20px; /* This is the space below the line */
+    padding-bottom: 15px; /* This is the space between the heading text and the line */
+  }
+  
+  #leftoffcanvas-button {
+    left: 400px;
+  }
+  
+  #rightoffcanvas-button {
+    right: 200px;
+  }
+  
+  #rightoffcanvas {
+    width: 200px;
+  }
+  
+  #left {
+    overflow-y: auto; 
+    /* max-height: calc(100vh - 128px); */
+    height: calc(100vh - 128px);
+  }
+  
+  .dropdown-toggle::after { 
+    content: none; 
+  } 
+  
+  .offcanvas-body {
+    overflow: hidden;
+  }
+  
+  .dropdown-menu {
+    max-height: 200px;
+    overflow-y: auto;
+  }
+  
+  .modal-dialog,
+  .modal-content {
+    /* 80% of window height */
+    height: 80%;
+  }
+  
+  .modal-body {
+    /* 100% = dialog height, 120px = header + footer */
+    max-height: calc(100vh - 210px);
+    overflow-y: auto;
+  }
+  
+  #right {
+    overflow-y: auto;
+    max-height: 100%;
+  }
+  
+  
+  .btn-bot{
+    position: absolute;
+    top:0px;
+    left:50%;
+    -ms-transform: translateX(-50%);
+    transform: translateX(-50%);
+  }
+  
+  .right {
+    overflow-y: scroll; 
+  }
+
+  #node_basics_table, #node_functions_table, #node_sequence_alignments_table {
+      font-size: x-small;
+  }
+
+  #node_basics_table {
+      text-align: center;
+  }
+
+  .modal_header {
+    font-variant: small-caps;
+    font-size: x-large;
+    background: linear-gradient(88deg, #f1f8ff, #ffffff);
+    padding-left: 10px;
+    margin-top: 20px;
+    margin-bottom: 5px;
+  }
+
+  .gene_cluster_context_items {
+    display: block;
+    border: 1px #dee2e6 solid;
+    padding: 0px 3px;
+    font-size: x-small;
+    background: #f2f2f2;
+  }
+
+  .gene_cluster_id {  
+    display: inline-block;
+    margin: 5px 2px;
+    padding: 3px 5px;
+    border: 1px solid #9c9c9c;
+    border-radius: 6px;
+    font-family: monospace;
+    background: #fff0f1;
+  }
+
+  .gene_cluster_id_current {
+      background: #d8ebde;
+  }
+
+  .bin-icon-size{
+    font-size: 14px;
+  }
+
+  #panel-left {
+    z-index: 2;
+  }
+
+  #toggle-panel-left{
+    z-index: 1;
+  }
+
+  #toggle-panel-top{
+    z-index: 1;
+  }
+
+  #title-panel{
+    z-index: 1;
+  }
+
+  #title-alter-panel{
+    z-index: 1;
+  }
+
+  .user-handle:hover{
+    background: var(--secondary-100);
+  }
+
+  .tableFixHead          { overflow: auto; height: 100px; }
+  .tableFixHead thead th { position: sticky; top: 0; z-index: 1; }
+
+  /* Just common table stuff. Really. */
+  /* table  { border-collapse: collapse; width: 100%; }
+  th, td { padding: 8px 16px; }
+  th     { background:#eee; } */
+
+  #InfoModalBody > .card-body {
+    padding-top: 0;
+  }
+
+  #gc-alignment-font span{
+    font-family: monospace !important;
+  }
+
+  #gc-alignment-font{
+    background-color: #e4e4e4;
+  }
+
+  #td-genome-cell{
+    position: sticky; 
+    left: 0; 
+    background-color: #e4e4e4; 
+    z-index: 2;
+    width: min-content;
+  }
+
+ #td-value-cell{
+    position: sticky; 
+    background-color: #e4e4e4;
+    z-index: 1;
+    display: flex;
+    align-items: center;
+    justify-content: center;
+ }
+
+#td-contig-cell{
+  position: sticky; 
+  background-color: #e4e4e4;
+  z-index: 1;
+ }
+
+#td-direction-cell{
+  position: sticky; 
+  background-color: #e4e4e4;
+  z-index: 1;
+  display: flex;
+  align-items: center;
+  justify-content: center;
+ }
+
+.td-analysis-cell-0{
+  background-color: red;
+}
+
+.td-analysis-cell-1{
+  background-color: green; 
+}
+
+
+.scroll-wrapper {
+  overflow-x: auto;
+  max-height: 200px;
+}
+
+.scrollable-content {
+  overflow-x: auto;
+  white-space: nowrap;
+  background-color: #e4e4e4;
+}
+
+#th-sequence{
+  position: sticky;
+  left: 25%;
+  z-index: 7;
+}
+
+.gc-table-header{
+  position: sticky;
+  top: 0;
+  z-index: 6;
+}
\ No newline at end of file
diff --git a/anvio/data/interactive/js/pangraph.js b/anvio/data/interactive/js/pangraph.js
new file mode 100644
index 000000000..16c7bdf6c
--- /dev/null
+++ b/anvio/data/interactive/js/pangraph.js
@@ -0,0 +1,2804 @@
+//ANCHOR - Constants
+const mapAS = {
+  'A': '<span style="color: #000000;">A</span>', 'R': '<span style="color: #ff0000;">R</span>',
+  'N': '<span style="color: #000000;">N</span>', 'D': '<span style="color: #000000;">D</span>',
+  'C': '<span style="color: #000000;">C</span>', 'Q': '<span style="color: #000000;">Q</span>',
+  'E': '<span style="color: #000000;">E</span>', 'G': '<span style="color: #ffa500;">G</span>',
+  'H': '<span style="color: #ff0000;">H</span>', 'I': '<span style="color: #00ff00;">I</span>',
+  'L': '<span style="color: #00ff00;">L</span>', 'K': '<span style="color: #ff0000;">K</span>',
+  'M': '<span style="color: #00ff00;">M</span>', 'F': '<span style="color: #00ff00;">F</span>',
+  'P': '<span style="color: #ffa500;">P</span>', 'S': '<span style="color: #ffa500;">S</span>',
+  'T': '<span style="color: #ffa500;">T</span>', 'W': '<span style="color: #00ffff;">W</span>',
+  'Y': '<span style="color: #00ffff;">Y</span>', 'V': '<span style="color: #00ff00;">V</span>',
+  '-': '<span style="color: #000000;">-</span>'
+};
+
+// we will fill this later from the incoming data
+var functional_annotation_sources_available = [];
+//ANCHOR - Bin creation
+var bins = {"bin1": []};
+var binnum = 1;
+
+var current_groups = {}
+
+// NOTE - From https://stackoverflow.com/questions/1053843/get-the-element-with-the-highest-occurrence-in-an-array
+function modeString(array) {
+  if (array.length == 0) return null;
+
+  var modeMap = {},
+    maxEl = array[0],
+    maxCount = 1;
+
+  for (var i = 0; i < array.length; i++) {
+    var el = array[i];
+
+    if (modeMap[el] == null) modeMap[el] = 1;
+    else modeMap[el]++;
+
+    if (modeMap[el] > maxCount) {
+      maxEl = el;
+      maxCount = modeMap[el];
+    } else if (modeMap[el] == maxCount && maxCount == 1) {
+      maxEl = el;
+      maxCount = modeMap[el];
+    } else if (modeMap[el] == maxCount) {
+      maxEl += ' & ' + el;
+      maxCount = modeMap[el];
+    }
+  }
+  return [maxEl, Math.round(maxCount/i * 100)];
+}
+
+function get_passed_gene_clusters(searchfunction) {
+  
+  var d = $.ajax({
+    url: "/pangraph/filter",
+    type: "POST",
+    data: JSON.stringify(searchfunction),
+    contentType: "application/json",
+    dataType: "json"
+  })
+
+  return d
+}
+
+//ANCHOR - Fetch GC consensus functions
+function get_gene_cluster_consensus_functions(gene_cluster_name) {
+
+  var func = new Object();
+  func['genecluster'] = gene_cluster_name
+
+  var d = $.ajax({
+    url: "/pangraph/function",
+    type: "POST",
+    data: JSON.stringify(func),
+    contentType: "application/json",
+    dataType: "json"
+  })
+
+  return d
+}
+
+function get_layer_data(gene_cluster_id, data, add_align) {
+
+  var layers = Object.keys(data['infos']['layers_data'])
+  var basic_info = {}
+
+  for (var layer_name of layers) {
+    if ($('#flex' + layer_name).prop('checked') == true){
+
+      basic_info[layer_name] = data['elements']['nodes'][gene_cluster_id]['layer'][layer_name]
+
+    }
+  }
+
+  if (add_align == 1) {
+    basic_layer_table = `<p class="modal_header mt-0">Layers</p>`;
+    basic_layer_table += `<table class="table table-striped table-bordered sortable" id="node_layers_table">`;
+  } else {
+    basic_layer_table = ''
+    basic_layer_table += `<table class="table table-striped table-bordered sortable">`;
+  }
+
+  basic_layer_table += `<tbody>`;
+  basic_layer_table += `<thead class="thead-light"><tr>`;
+  for (const [key, value] of Object.entries(basic_info)) {
+    basic_layer_table += `<th scope="row">` + key + `</th>`;
+  }
+  basic_layer_table += `</tr></thead><tbody>`;
+
+  basic_layer_table += `<tbody><tr>`;
+  for (const [key, value] of Object.entries(basic_info)) {
+    basic_layer_table += `<td>` + value + `</td>`;
+  }
+  basic_layer_table += `</tbody></tr></table>`;
+
+  return basic_layer_table;
+
+}
+
+function get_gene_cluster_basics_table(gene_cluster_id, gene_cluster_context, data, add_align) {
+    // first, learn a few basics about the gene cluster to be displayed
+    var x_pos = data['elements']['nodes'][gene_cluster_id]['position']['x_offset']
+    // var position_in_graph = x_pos + " / " + (data["infos"]["meta"]["global_x_offset"] - 1);
+    var position_in_graph = x_pos;
+    // var num_contributing_genomes = Object.keys(data['elements']['nodes'][gene_cluster_id]['genome']).length + " / " + (data['infos']['num_genomes']);
+    var num_contributing_genomes = Object.keys(data['elements']['nodes'][gene_cluster_id]['genome']).length;
+    var gene_cluster_name = data['elements']['nodes'][gene_cluster_id]['name']
+
+    if (gene_cluster_context == null){
+      var context = gene_cluster_id
+    } else {
+      var context = gene_cluster_context
+    }
+
+    basic_info = {'ID': gene_cluster_id, 'Gene Cluster': gene_cluster_name, 'Contributing Genomes': num_contributing_genomes, 'Position in Graph': position_in_graph}
+    // build the basic information table
+    if (add_align == 1) {
+      basic_info_table = `<p class="modal_header mt-0">Basics</p>`;
+      basic_info_table += `<table class="table table-striped table-bordered sortable" gc_context="` + context + `" gc_pos="` + x_pos + `" gc_id="` + gene_cluster_id + `" id="node_basics_table">`;
+    } else {
+      basic_info_table = ''
+      basic_info_table += `<table class="table table-striped table-bordered sortable">`;
+    }
+
+    basic_info_table += `<tbody>`;
+    basic_info_table += `<thead class="thead-light"><tr>`;
+    for (const [key, value] of Object.entries(basic_info)) {
+        basic_info_table += `<th scope="row">` + key + `</th>`;
+    }
+    basic_info_table += `</tr></thead><tbody>`;
+
+    basic_info_table += `<tbody><tr>`;
+    for (const [key, value] of Object.entries(basic_info)) {
+        basic_info_table += `<td>` + value + `</td>`;
+    }
+    basic_info_table += `</tbody></tr></table>`;
+
+    return basic_info_table;
+}
+
+
+async function get_gene_cluter_functions_table(gene_cluster_id, data, add_alig) {
+    
+    if (add_align == 1) {
+      functions_table = `<p class="modal_header">Consensus functional annotations</p>`;
+      functions_table += `<table class="table table-striped sortable" gc_id="` + gene_cluster_id + `" id="node_functions_table">`;
+    } else {
+      functions_table = ''
+      functions_table += `<table class="table table-striped sortable">`;
+    }
+    functions_table += `<thead><tr>`;
+    functions_table += `<th scope="col">Source</th>`;
+    functions_table += `<th scope="col">Accession</th>`;
+    functions_table += `<th scope="col">Function</th>`;
+    functions_table += `</tr></thead><tbody>\n\n`;
+
+    var gene_cluster_name = data['elements']['nodes'][gene_cluster_id]['name']
+    var d = await get_gene_cluster_consensus_functions(gene_cluster_name);
+
+    // console.log(d)
+
+    function_sources = Object.keys(d).sort();
+    // console.log(function_sources);
+    for (source of function_sources) {
+        value = d[source];
+        // console.log(source)
+        var accession = value['accession']
+        accession === undefined | accession === null ? accession = '' : accession = accession
+        var func = value['function']
+        func === undefined | func === null ? func = '' : func = func
+
+        functions_table += `<tr>`;
+        functions_table += `<td>` + source + `</td>`;
+        functions_table += `<td>` + accession + `</td>`;
+        functions_table += `<td>` + func + `</td>`;
+        functions_table += `</tr>`;
+    }
+    functions_table += `</tbody></tr></table>\n\n`;
+
+    return functions_table
+}
+
+
+function get_gene_cluster_context_table(gene_cluster_id_current, gene_cluster_context, data, add_align) {
+    
+    if (gene_cluster_context == null){
+        return '';
+    } else {
+      var group_context = []
+      for (item in data['infos']['groups'][gene_cluster_context]){
+        group_context.push(data['infos']['groups'][gene_cluster_context][item])
+      }
+    }
+
+    // console.log(gene_cluster_id_current, gene_cluster_context, group_context)
+    if (add_align == 1) {
+      gene_cluster_context_table = `<p class="modal_header">Gene cluster context</p>`;
+    }else {
+      gene_cluster_context_table = ''
+    }
+    gene_cluster_context_table += `<div class="gene_cluster_context_items">`;
+    for(index in group_context) {
+        gene_cluster_id = group_context[index];
+        gene_cluster_name = data['elements']['nodes'][gene_cluster_id]['name']
+
+        if (gene_cluster_id == gene_cluster_id_current){
+            gene_cluster_context_table += `<span class="gene_cluster_id gene_cluster_id_current">` + gene_cluster_name + `</span>`;
+        } else {
+            gene_cluster_context_table += `<span class="gene_cluster_id"><a class="btn border-0 m-0 p-0 align-baseline group_choice" context="` + add_align + `" group="` + gene_cluster_context + `" name_id="` + gene_cluster_id + `">` + gene_cluster_name + `</a></span>`;
+        }
+    }
+    gene_cluster_context_table += `</div>`;
+
+    return gene_cluster_context_table;
+
+}
+
+
+//ANCHOR - Get tables for GC basic info and functions
+async function get_gene_cluster_display_tables(gene_cluster_id, gene_cluster_context, data, add_align) {
+    // The purpose of this function is to build HTML formatted tables to give access to
+    // the details of a gene cluster. The parameters here are,
+    //
+    //   - `gene_cluster_id`: A singular gene cluster id to be detailed,
+    //   - `gene_cluster_context`: A list of gene cluster ids that occur in the same context
+    //      with `gene_cluster_id` (either they were binned together, or they were in the same
+    //      group of gene clusters).
+    //   - `data`: the primary data object from the JSON input
+    //
+    // If everything goes alright, this function will return a table that can be displayed in
+    // any modal window.
+    ///////////////////////////////////////////////////////////////////////////////////////////
+    // BUILD CONTEXT
+    // if this is a gene cluster that is a part of a context, then all others are going to be
+    // shown here
+    ///////////////////////////////////////////////////////////////////////////////////////////
+
+    gene_cluster_context_table = get_gene_cluster_context_table(gene_cluster_id, gene_cluster_context, data, add_align);
+
+    ///////////////////////////////////////////////////////////////////////////////////////////
+    // BUILD BASIC INFORMATION TABLE
+    ///////////////////////////////////////////////////////////////////////////////////////////
+
+    basic_info_table = get_gene_cluster_basics_table(gene_cluster_id, gene_cluster_context, data, add_align);
+
+    ///////////////////////////////////////////////////////////////////////////////////////////
+    // BUILD FUNCTIONS TABLE
+    ///////////////////////////////////////////////////////////////////////////////////////////
+
+    basic_layer_table = get_layer_data(gene_cluster_id, data, add_align);
+
+    functions_table = await get_gene_cluter_functions_table(gene_cluster_id, data, add_align);
+
+    ///////////////////////////////////////////////////////////////////////////////////////////
+    // RETRIEVE AND BUILD SEQUENCE ALIGNMENTS
+    ///////////////////////////////////////////////////////////////////////////////////////////
+ 
+    if (add_align == 1) {
+
+      var alignment = {}
+
+      // if (gene_cluster_id != 'start' && gene_cluster_id != 'stop') {
+      for (var genome of Object.keys(data['elements']['nodes'][gene_cluster_id]['genome'])) {
+        
+        // if ($('#flex' + genome).prop('checked') == true){
+        
+        var genecall = data['elements']['nodes'][gene_cluster_id]['genome'][genome]['gene_call']
+        var contig = data['elements']['nodes'][gene_cluster_id]['genome'][genome]['contig']
+        var direction = data['elements']['nodes'][gene_cluster_id]['genome'][genome]['direction']
+        var name = data['elements']['nodes'][gene_cluster_id]['name']
+        alignment[genome] = [genecall, contig, direction, name]
+
+        // }
+      }
+      // }
+
+      gene_cluster_sequence_alignments_table = await appendalignment(gene_cluster_id, alignment)
+
+      ///////////////////////////////////////////////////////////////////////////////////////////
+      // MERGE ALL AND RETURN
+      ///////////////////////////////////////////////////////////////////////////////////////////
+
+      return gene_cluster_context_table + basic_info_table + basic_layer_table + functions_table + gene_cluster_sequence_alignments_table
+
+    } else {
+
+      return gene_cluster_context_table + basic_info_table + basic_layer_table + functions_table
+
+    }
+}
+
+//ANCHOR - Fetch GC alignment
+function fetchalignment(alignment) {
+
+  var d = $.ajax({
+    url: "/pangraph/alignment",
+    type: "POST",
+    data: JSON.stringify(alignment),
+    contentType: "application/json",
+    dataType: "json"
+  })
+
+  return d
+
+};
+
+//ANCHOR - Append GC alignment
+async function appendalignment(gene_cluster_id, alignment) {
+    // FIXME: We need to come up with more accurate and explicit function names.
+    if (Object.keys(alignment).length == 0) {
+        return ''
+    }
+
+    alignments_table = `<p class="modal_header">Sequence alignments</p>`;
+    alignments_table += `<div class="scroll-wrapper"><table class="table sortable" gc_id="` + gene_cluster_id + `" id="node_sequence_alignments_table">`;
+    alignments_table += `<thead class="thead-dark gc-table-header"><tr>`;
+    alignments_table += `<th class="position-sticky" style="left:0px; z-index:2;" scope="col">Genome</th>`;
+    alignments_table += `<th scope="col">Gene Call</th>`;
+    alignments_table += `<th scope="col">Contig</th>`;
+    alignments_table += `<th scope="col">Direction</th>`;
+    alignments_table += `<th scope="col"><span id="th-sequence">Sequence</span></th>`;
+    alignments_table += `</tr></thead><tbody>\n\n`;
+
+
+    var d = await fetchalignment(alignment)
+
+    // console.log(d)
+
+    for (var [genome, value] of Object.entries(d)) {
+      var colored = value[3].replace(/A|R|N|D|C|Q|E|G|H|I|L|K|M|F|P|S|T|W|Y|V|-/gi, function(matched){return mapAS[matched];});
+
+      alignments_table += `<tr>`
+      alignments_table += `<td id="td-genome-cell">` + genome + `</td>`
+      alignments_table += `<td id="td-value-cell">` + value[0] + `</a></td>`
+      alignments_table += `<td id="td-contig-cell">` + value[1] + `</td>`
+      alignments_table += `<td id="td-direction-cell">` + value[2] + `</a></td>`
+      alignments_table += `<td id="gc-alignment-font"><div class="scrollable-content">` + colored + `</div></td>`
+      alignments_table += `</tr>`
+    }
+
+    alignments_table += `</tbody></table></div>\n\n`
+
+    // I guess this shouldn't return anything but insert the results into a context?
+    // lol sorry if I screwed these thigns up badly :) IDK what I'm doing :p
+    return alignments_table;
+}
+
+//ANCHOR - Color node and add/remove from bin
+function marknode(e, data, binid, bins){
+
+  var bincolor = document.getElementById(binid + 'color').value
+  var id = e.id;
+  var current = ''
+
+  var binkeys = Object.keys(bins)
+    for (var key of binkeys) {
+      if (bins[key].includes(id)) {
+        current = key
+        break;
+    }
+  }
+
+  if ($('#flexsaturation').prop('checked') == true){
+    var saturation = 1
+  } else {
+    var saturation = 0
+  }
+
+  if (e.getAttribute('class') == 'group') {
+
+    var node_color = $('#groups')[0].value;
+    var genome_size = Object.keys(data["infos"]["genomes"]).length;
+
+    var group = data['infos']['groups'][id]
+    var node_name = group[0]
+
+    var node = data['elements']['nodes'][node_name];
+    var genome = Object.keys(node['genome']).length;
+
+  } else if (e.getAttribute('class') == 'node') {
+
+    var node_color = $('#nodes')[0].value;
+    var genome_size = Object.keys(data["infos"]["genomes"]).length;
+
+    var node = data['elements']['nodes'][id];
+    var genome = Object.keys(node['genome']).length;
+
+  }
+
+  if (current === binid) {
+
+    if (saturation == 1){
+      e.setAttribute("fill", lighter_color('#ffffff', node_color, genome / genome_size))
+    } else {
+      e.setAttribute("fill", node_color)
+    }
+    
+    bins[binid] = bins[binid].filter(item => item !== id)
+    $('#' + binid + 'value')[0].value = bins[binid].length
+
+  } else if (current === '') {
+
+    if (saturation == 1){
+      e.setAttribute("fill", lighter_color('#ffffff', bincolor, genome / genome_size))
+    } else {
+      e.setAttribute("fill", bincolor)
+    }
+
+    bins[binid].push(id)
+    $('#' + binid + 'value')[0].value = bins[binid].length
+
+  } else {
+
+    if (saturation == 1){
+      e.setAttribute("fill", lighter_color('#ffffff', bincolor, genome / genome_size))
+    } else {
+      e.setAttribute("fill", bincolor)
+    }
+
+    bins[current] = bins[current].filter(item => item !== id)
+    bins[binid].push(id)
+    $('#' + binid + 'value')[0].value = bins[binid].length
+    $('#' + current + 'value')[0].value = bins[current].length
+
+  }
+
+  return bins
+}
+
+// //ANCHOR - Information for the GC
+async function nodeinfo(e, data) {
+  var id = e.id;
+  var element = document.getElementById(id);
+
+  if (element.getAttribute('class') == 'group') {
+    gene_cluster_context = id;
+    gene_cluster_id = data['infos']['groups'][id][0]
+  } else {
+    gene_cluster_id = id;
+    gene_cluster_context = null;
+  }
+
+  $('#InfoModalBody').empty()
+  var bodyinfo = $('<div class="card-body overflow-scroll"></div>')
+  // var closeBtn = $('<div class="row justify-content-end"><i class="btn d-flex col-1 justify-content-end text-danger fs-2x bi bi-x-circle-fill" data-dismiss="modal"></i></div>')
+  // $('#InfoModalBody').append(closeBtn)
+  $('#InfoModalBody').append(bodyinfo)
+
+  // console.log(gene_cluster_id, gene_cluster_context)
+
+  var all_info = await get_gene_cluster_display_tables(gene_cluster_id, gene_cluster_context, data, add_align=1)
+
+  // console.log(all_info)
+
+  bodyinfo.append(all_info)
+
+  $('#InfoModal').modal('show');
+}
+
+//ANCHOR - Degree to rad calculation
+function deg2rad(degrees)
+{
+  return degrees * Math.PI/180;
+}
+
+//ANCHOR - General download function
+function downloadBlob(blob, name) {
+
+  var blobUrl = URL.createObjectURL(blob);
+  var link = document.createElement("a");
+
+  link.href = blobUrl;
+  link.download = name;
+
+  document.body.appendChild(link);
+
+  link.dispatchEvent(
+    new MouseEvent('click', {
+      bubbles: true,
+      cancelable: true,
+      view: window
+    })
+  );
+
+  document.body.removeChild(link);
+}
+
+// NOTE - From https://coderwall.com/p/z8uxzw/javascript-color-blender
+function int_to_hex(num) {
+    var hex = Math.round(num).toString(16);
+    if (hex.length == 1)
+        hex = '0' + hex;
+    return hex;
+}
+
+//ANCHOR - Function to mix two colors
+function lighter_color(color1, color2, percentage, threshold=0.25) {
+
+  // console.log(color1, color2, percentage)
+
+  percentage = threshold + (1 - threshold) * percentage
+
+  // var color3 = $.xcolor.gradientlevel(color1, color2, percentage, 1);
+
+  color1 = color1.substring(1);
+  color2 = color2.substring(1);
+
+  color1 = [parseInt(color1[0] + color1[1], 16), parseInt(color1[2] + color1[3], 16), parseInt(color1[4] + color1[5], 16)];
+  color2 = [parseInt(color2[0] + color2[1], 16), parseInt(color2[2] + color2[3], 16), parseInt(color2[4] + color2[5], 16)];
+
+  var color3 = [
+      (1 - percentage) * color1[0] + percentage * color2[0],
+      (1 - percentage) * color1[1] + percentage * color2[1],
+      (1 - percentage) * color1[2] + percentage * color2[2]
+  ];
+
+  color3 = '#' + int_to_hex(color3[0]) + int_to_hex(color3[1]) + int_to_hex(color3[2]);
+
+  // console.log(color3)
+
+  return color3
+}
+
+function create_rectangle(i_x, i_y, j_x, j_y, theta, node_distance_x, linear, color, id='') {
+
+  if (id != '') {
+    var extra = '" id="' + id
+  } else {
+    var extra = ''
+  }
+
+  if (linear == 0) {
+    var [a_x, a_y] = transform(i_x, i_y, theta)
+    var [b_x, b_y] = transform(j_x, i_y, theta)
+    var [c_x, c_y] = transform(i_x, j_y, theta)
+    var [d_x, d_y] = transform(j_x, j_y, theta)
+
+    var path = $('<path d="' +
+      'M ' + a_x + ' ' + a_y + ' ' +
+      'A ' + (i_y) + ' ' + (i_y) + ' 0 0 0 ' + b_x + ' ' + b_y + ' ' +
+      'L' + d_x + ' ' + d_y +  ' ' +
+      'A ' + (j_y) + ' ' + (j_y) + ' 0 0 1 ' + c_x + ' ' + c_y + ' ' +
+      'L' + a_x + ' ' + a_y +
+      '" fill="' + color + extra + '" stroke="" stroke-width="0"/>')
+  } else {
+    var [a_x, a_y] = [i_x * node_distance_x, -i_y]
+    var [b_x, b_y] = [j_x * node_distance_x, -i_y]
+    var [c_x, c_y] = [i_x * node_distance_x, -j_y]
+    var [d_x, d_y] = [j_x * node_distance_x, -j_y]
+  
+    var path = $('<path d="' +
+      'M ' + a_x + ' ' + a_y + ' ' +
+      'L ' + b_x + ' ' + b_y + ' ' +
+      'L ' + d_x + ' ' + d_y +  ' ' +
+      'L ' + c_x + ' ' + c_y + ' ' +
+      'L' + a_x + ' ' + a_y +
+      '" fill="' + color + extra + '" stroke="" stroke-width="0"/>')
+  }
+
+  return(path)
+}
+
+//ANCHOR - Transformation function
+function transform(x, y, theta) {
+  var circle_x = y * Math.sin(deg2rad(theta * x))
+  var circle_y = y * Math.cos(deg2rad(theta * x))
+  return [circle_x, circle_y]
+}
+
+function pickcolor (edgecoloring, genomes) {
+
+  var array = []
+
+  for (var name of genomes) {
+    array.push(edgecoloring[name])
+    var sortedArray = array.sort(function(a, b) {
+      return a[0] - b[0];
+    });
+  }
+
+  return sortedArray[0][1]
+}
+
+function draw_newick(order, item_dist, max_dist, offset, max_size, line_thickness) {
+
+  var output = ''
+  var saving_positions = {}
+  var saving_ids = {}
+  
+  var i = 0
+  
+  for (var [item, start, end] of order){
+  
+    var start_fraction = (max_size * (start / max_dist) - max_size) - offset
+    var end_fraction = (max_size * (end / max_dist) - max_size) - offset
+    
+    if (item != 'branching') {
+      var y_value = item_dist[item]
+      output += '<path d="M ' + start_fraction + ' ' + y_value + ' L ' + end_fraction + ' ' + y_value + '" stroke-width="' + line_thickness + '" stroke="black"></path>'
+
+      if (Object.values(saving_ids).includes(start_fraction)){
+        var saving_id = Object.keys(saving_ids)[Object.values(saving_ids).indexOf(start_fraction)]
+        // console.log(saving_id)
+        saving_positions[saving_id].push(y_value)
+      } else {
+        saving_ids[i] = start_fraction
+        saving_positions[i] = [y_value]
+        i = i + 1
+      }
+      if (end_fraction != max_size){
+        output += '<path d="M ' + end_fraction + ' ' + y_value + ' L ' + (0 - offset) + ' ' + y_value + '" stroke-dasharray="' + line_thickness * 5 + ',' + line_thickness * 5 + '" stroke-width="' + line_thickness + '" stroke="lightgray"></path>'
+      }
+    } else {
+
+      if (Object.values(saving_ids).includes(end_fraction)){
+        var saving_id_main = Object.keys(saving_ids)[Object.values(saving_ids).indexOf(end_fraction)]
+        sorted_positions = saving_positions[saving_id_main].sort()
+        // console.log(sorted_positions)
+        
+        // for (var j in sorted_positions) {
+        for (var j = 0; j < sorted_positions.length -1; j++) {
+          
+          var y_value_i = sorted_positions[j]
+          var y_value_j = sorted_positions[j+1]
+        
+          output += '<path d="M ' + end_fraction + ' ' + y_value_i + ' L ' + end_fraction + ' ' + y_value_j + '" stroke-width="' + line_thickness + '" stroke="black"></path>'
+
+        }
+      } else {
+        var saving_id_main = -1
+      }
+
+      y_value = Math.min(...sorted_positions) + (Math.max(...sorted_positions) - Math.min(...sorted_positions)) / 2
+      output += '<path d="M ' + start_fraction + ' ' + y_value + ' L ' + end_fraction + ' ' + y_value + '" stroke-width="' + line_thickness + '" stroke="black"></path>'
+
+      if (Object.values(saving_ids).includes(start_fraction)) {
+        var saving_id = Object.keys(saving_ids)[Object.values(saving_ids).indexOf(start_fraction)]
+        saving_positions[saving_id].push(y_value)
+      } else {
+        saving_ids[i] = start_fraction
+        saving_positions[i] = [y_value]
+        i = i + 1
+      }
+
+      if (saving_id_main != -1) {
+        delete saving_ids[saving_id_main]
+        delete saving_positions[saving_id_main]
+      }
+    }
+  }
+  return(output)
+
+}
+
+function newick_to_order(string, prior = 0) {
+  var result = []
+  var newick = string.replace(' ', '')
+
+  if (newick[0] == '('){
+    var bracket_open = 0
+    var bracket_closed = 0
+
+    // for (var i in newick) {
+    for (var i = 0; i < newick.length; i++) {
+
+      var sub_letter = newick[i]
+      if (sub_letter == '(') {
+        bracket_open += 1 
+      } else if (sub_letter == ')') {
+        bracket_closed += 1
+      }
+          
+      if (bracket_open == bracket_closed) {
+        
+        var sub_newick = newick.slice(1, i)
+        var rest = newick.slice(i)
+        
+        if (rest.includes(',')) {
+            var parts = rest.split(',')
+            if (parts[0].includes(':')) {
+                var value = parts[0].split(':')[1]
+            } else {
+                var value = 0 
+            }
+
+            result.push(...[['branching', prior, prior + parseFloat(value)]])
+
+            // console.log(sub_newick)
+            result.push(...newick_to_order(sub_newick, prior + parseFloat(value)))
+            
+            var next_iter = parts.slice(1).join(',')
+            // console.log(next_iter)
+            result.push(...newick_to_order(next_iter, prior))
+        } else {
+            if (rest.includes(':')) {
+                var value = rest.split(':').slice(1)
+            } else {
+                var value = 0 
+            }
+            result.push(...[['branching', prior, prior + parseFloat(value)]])
+            // console.log(sub_newick)
+            result.push(...newick_to_order(sub_newick, prior + parseFloat(value)))
+        }
+        break;
+
+      }
+
+    }
+
+  } else {
+
+    if (newick.includes(',')) {
+      var parts = newick.split(',')
+      if (parts[0].includes(':')){
+        var value = parts[0].split(':')[1]
+        var branch = parts[0].split(':')[0]
+      } else {
+        var value = 0 
+        var branch = parts[0]
+      }
+
+      var next_iter = parts.slice(1).join(',')
+      result.push(...[[branch, prior, prior + parseFloat(value)]])
+      // console.log(next_iter)
+      result.push(...newick_to_order(next_iter, prior))
+
+    } else{ 
+      if (newick.includes(':')) {
+        var value = newick.split(':')[1]
+        var branch = newick.split(':')[0]
+      } else {
+        var value = 0 
+        var branch =  newick
+      }
+      result.push(...[[branch, prior, prior + parseFloat(value)]])
+    }
+  }
+
+  return(result)
+}
+
+//ANCHOR - All in one SVG creation function
+async function generate_svg(body, data) {
+
+  // access all the relevant variables from UI
+
+  var svg_search = [];
+  var svg_heatmaps = [];
+  var svg_edges = [];
+  var svg_nodes = [];
+  var svg_groups = [];
+
+  var edgecoloring = {}
+  $("#genomecolors :input[type='color']").each((index, element) => {
+    edgecoloring[element.id] = [index, element.value]
+  })
+
+  if ($('#flexlinear').prop('checked') == true){
+    var linear = 1
+  } else {
+    var linear = 0
+  }
+
+  if ($('#flexsaturation').prop('checked') == true){
+    var saturation = 1
+  } else {
+    var saturation = 0
+  }
+
+  var outer_margin = parseInt($('#outer_margin')[0].value);
+  var inner_margin = parseInt($('#inner_margin')[0].value);
+  var node_size = parseInt($('#size')[0].value);
+  var node_thickness = parseInt($('#circ')[0].value);
+  var edge_thickness = parseInt($('#edge')[0].value);
+  var line_thickness = parseInt($('#line')[0].value);
+  var node_distance_x = parseInt($('#distx')[0].value);
+  var node_distance_y = parseInt($('#disty')[0].value);
+  var tree_length = parseInt($('#tree')[0].value);
+  var offset = parseInt($('#tree_offset')[0].value);
+  var tree_thickness = parseInt($('#tree_thickness')[0].value);
+
+  var groups = data['infos']['groups']
+  var edges = data['elements']['edges']
+  var nodes = data['elements']['nodes']
+
+  var global_x = data["infos"]["meta"]["global_x_offset"] -1;
+  var global_y = data["infos"]["meta"]["global_y"] +1;
+
+  var group_color = $('#groups')[0].value;
+  var node_color = $('#nodes')[0].value;
+  var layer_color = $('#layer_color')[0].value;
+
+  var theta = 270 / (global_x)
+  var start_offset = parseInt($('#inner')[0].value);
+  // var start_offset = 0
+  
+  var middle_layers = new Object();
+  var outer_layers = new Object();
+
+  var search_size = parseInt($('#search_hit')[0].value);
+  middle_layers['search'] = [search_size, start_offset, search_size + start_offset]
+
+  var arrow_size = parseInt($('#arrow')[0].value)
+  middle_layers['arrow'] = [arrow_size, search_size + start_offset, arrow_size + search_size + start_offset]
+
+  var graph_size = node_size * 2 + node_thickness
+  outer_layers['graph'] = [graph_size, inner_margin, inner_margin + graph_size]
+
+  var sum_middle_layer = start_offset + search_size + arrow_size
+  var sum_outer_layer = graph_size + inner_margin
+
+  var current_middle_stop = sum_middle_layer
+  var current_outer_stop = sum_outer_layer
+
+  var genomes = Object.keys(data["infos"]["genomes"])
+  var enabled = []
+
+  var genome_size = genomes.length;
+
+  var order = newick_to_order(data['infos']['newick']).reverse()
+
+  max_dist = 0
+  item_order = []
+  for (var item of order) {
+    var [name, start, end] = item
+    if (name != 'branching') {
+      item_order.push(name)
+    }
+    if (end > max_dist) {
+      max_dist = end
+    }
+  }
+
+// layer size calculations
+
+  for (var genome of item_order) {
+
+    if ($('#flex' + genome).prop('checked') == true){
+      enabled.push(genome)
+    }
+
+    var layer_name = genome + 'layer'
+    if ($('#flex' + layer_name).prop('checked') == true){
+      var layer_width = parseInt($('#' + layer_name)[0].value)
+
+      var layer_middle_start = current_middle_stop + inner_margin
+      var layer_middle_stop = layer_middle_start + layer_width
+
+      current_middle_stop = layer_middle_stop
+      sum_middle_layer += layer_width + inner_margin
+      
+      middle_layers[layer_name] = [layer_width, layer_middle_start, layer_middle_stop]
+    }
+  }
+
+  var layers = Object.keys(data['infos']['layers_data'])
+  for (var layer_name of layers) {
+    if ($('#flex' + layer_name).prop('checked') == true){
+
+      var layer_width = parseInt($('#' + layer_name)[0].value)
+      // var layer_scale = data['infos']['layers_data'][layer_name]['scale']
+
+      // if (layer_scale == 'global') {
+      //   var layer_middle_start = current_middle_stop + inner_margin
+      //   var layer_middle_stop = layer_middle_start + layer_width
+
+      //   current_middle_stop = layer_middle_stop
+      //   sum_middle_layer += layer_width + inner_margin
+        
+      //   middle_layers[layer_name] = [layer_width, layer_middle_start, layer_middle_stop]
+      // } else {
+      var layer_outer_start = current_outer_stop + outer_margin
+      var layer_outer_stop = layer_outer_start + layer_width
+
+      current_outer_stop = layer_outer_stop 
+      sum_outer_layer += layer_width + outer_margin
+      
+      outer_layers[layer_name] = [layer_width, layer_outer_start, layer_outer_stop]
+      // }
+    }
+  }
+
+  if (linear == 0){
+    var radius = 0.5 * (node_distance_x / Math.sin(deg2rad(theta * (1/2))))
+    var circle_dist = sum_middle_layer + graph_size * 0.5
+    var extra_offset = 0
+
+    if (circle_dist < radius) {
+      extra_offset = radius - circle_dist
+    }
+
+    sum_middle_layer += extra_offset
+    for (var layer in middle_layers) {
+      var [layer_width, layer_start, layer_stop] = middle_layers[layer]
+      middle_layers[layer] = [layer_width, layer_start + extra_offset, layer_stop + extra_offset]
+    }
+
+    var y_size = (sum_middle_layer + (global_y * node_distance_y) + sum_outer_layer);
+    var x_size = (sum_middle_layer + (global_y * node_distance_y) + sum_outer_layer);
+    var svg_core = $('<svg id="result" width="100%" height="100%" version="1.1" viewBox="-' + x_size + ' -' + y_size + ' ' + x_size*2 + ' ' + y_size*2 + '" position="absolute" xmlns="http://www.w3.org/2000/svg">')
+  } else {
+    var x_size = global_x * node_distance_x;
+    var y_size = (sum_middle_layer + (global_y * node_distance_y) + sum_outer_layer);
+    var svg_core = $('<svg id="result" width="100%" height="100%" version="1.1" viewBox="-' + x_size*0.5 + ' -' + y_size*5 + ' ' + x_size*2 + ' ' + y_size*2 + '" position="absolute" xmlns="http://www.w3.org/2000/svg">')
+  }
+
+  for (var genome of genomes) {
+    var layer_name = genome + 'layer'
+    if (Object.keys(middle_layers).includes(layer_name)){
+
+      var [layer_width, layer_start, layer_stop] = middle_layers[layer_name]
+      for (var x = 1; x < global_x+1; x++) {
+
+        var add_start = 1
+        var add_stop = 0
+
+        var i_x = x-add_start
+        var i_y = layer_start
+        var j_x = x+add_stop
+        var j_y = layer_stop
+
+        // console.log(i_x, i_y, j_x, j_y)
+
+        svg_heatmaps.push(
+          create_rectangle(i_x, i_y, j_x, j_y, theta, node_distance_x, linear, layer_color)
+        )
+      }
+    }
+  }
+
+  // var [search_size, search_start, search_stop] = middle_layers['search']
+
+  // if (linear == 0){
+  //   var [circle_h_x, circle_h_y] = transform(0, search_start + search_size * 0.5, theta)
+  // } else {
+  //   var [circle_h_x, circle_h_y] = [0, -(search_start + search_size * 0.5)]
+  // }
+    
+  // svg_core.append(
+  //   $('<text text-anchor="end" transform="translate (-10)" dominant-baseline="middle" x="' + circle_h_x + '" y="' + circle_h_y + '" dy="0" font-size="' + $('#label')[0].value + '" font-family="sans-serif" fill="black">Search Hits</text>')
+  // )
+
+  if ($('#flexarrow').prop('checked') == true){
+    
+    var [arrow_size, arrow_start, arrow_stop] = middle_layers['arrow']
+
+    var pointer_length = 5/ theta
+    var pointer_height = arrow_stop - arrow_start
+    var arrow_thickness = pointer_height / 4
+    var steps = Math.round((30 / theta))
+
+    if (steps < 1) {
+      steps = 1
+    }
+
+    if (linear == 0){
+      var [circle_c_x, circle_c_y] = transform(global_x - pointer_length, arrow_start + arrow_thickness, theta)
+      var [circle_a_x, circle_a_y] = transform(0, arrow_start + arrow_thickness, theta)
+      var [circle_b_x, circle_b_y] = transform(0, arrow_stop - arrow_thickness, theta)
+      var [circle_d_x, circle_d_y] = transform(global_x - pointer_length, arrow_stop - arrow_thickness, theta)
+      var [circle_f_x, circle_f_y] = transform(global_x - pointer_length, arrow_stop, theta)
+      var [circle_g_x, circle_g_y] = transform(global_x, arrow_start + arrow_thickness * 2, theta)
+      var [circle_e_x, circle_e_y] = transform(global_x - pointer_length, arrow_start, theta)
+
+      if ((global_x) * theta >= 180) {
+        var arc_flag = 1
+      } else {
+        var arc_flag = 0
+      }
+
+      svg_core.append(
+        $('<path d="M ' + circle_c_x + ' ' + circle_c_y +
+        ' A ' + (arrow_start + arrow_thickness) + ' ' + (arrow_start + arrow_thickness) + ' 0 ' + arc_flag + ' 1 ' + circle_a_x + ' ' + circle_a_y +
+        ' L ' + circle_b_x + ' ' + circle_b_y +
+        ' A ' + (arrow_stop - arrow_thickness) + ' ' + (arrow_stop - arrow_thickness) + ' 0 ' + arc_flag + ' 0 ' + circle_d_x + ' ' + circle_d_y +
+        ' L ' + circle_f_x + ' ' + circle_f_y +
+        ' L ' + circle_g_x + ' ' + circle_g_y +
+        ' L ' + circle_e_x + ' ' + circle_e_y + 
+        ' Z" stroke-width="0" fill="slateGrey"></path>')
+      )
+
+      var [circle_h_x, circle_h_y] = transform(0, arrow_start + arrow_thickness * 2, theta)
+
+    } else {
+      var [circle_c_x, circle_c_y] = [(global_x - pointer_length) * node_distance_x, -(arrow_start + arrow_thickness)]
+      var [circle_a_x, circle_a_y] = [0, -(arrow_start + arrow_thickness)]
+      var [circle_b_x, circle_b_y] = [0, -(arrow_stop - arrow_thickness)]
+      var [circle_d_x, circle_d_y] = [(global_x - pointer_length) * node_distance_x , -(arrow_stop - arrow_thickness)]
+      var [circle_f_x, circle_f_y] = [(global_x - pointer_length) * node_distance_x, -arrow_stop]
+      var [circle_g_x, circle_g_y] = [global_x * node_distance_x, -(arrow_start + arrow_thickness * 2)]
+      var [circle_e_x, circle_e_y] = [(global_x - pointer_length) * node_distance_x, -arrow_start]
+
+      svg_core.append(
+        $('<path d="M ' + circle_c_x + ' ' + circle_c_y +
+        ' L ' + circle_a_x + ' ' + circle_a_y +
+        ' L ' + circle_b_x + ' ' + circle_b_y +
+        ' L ' + circle_d_x + ' ' + circle_d_y +
+        ' L ' + circle_f_x + ' ' + circle_f_y +
+        ' L ' + circle_g_x + ' ' + circle_g_y +
+        ' L ' + circle_e_x + ' ' + circle_e_y + 
+        ' Z" stroke-width="0" fill="slateGrey"></path>')
+      )
+
+      var [circle_h_x, circle_h_y] = [0, -(arrow_start + arrow_thickness * 2)]
+    }
+      
+    svg_core.append(
+      $('<text text-anchor="end" transform="translate (-10)" dominant-baseline="middle" x="' + circle_h_x + '" y="' + circle_h_y + '" dy="0" font-size="' + $('#label')[0].value + '" font-family="sans-serif" fill="black">Orientation</text>')
+    )
+
+    var l = steps
+    while (l < global_x) {
+
+      if (l+steps <= global_x){
+        var k = steps;
+      } else {
+        var k = steps - ((l+steps) - global_x);
+      }
+
+      if (linear == 0){
+
+        var [circle_l_x, circle_l_y] = transform(l-0.5, arrow_start + arrow_thickness * 2, theta)
+        var rotate = theta * (l-0.5)
+        if (rotate >= 90 && rotate <= 180) {
+          rotate += 180;
+        } else if (rotate >= 180 && rotate <= 270) {
+          rotate -= 180;
+        }
+        svg_core.append(
+          $('<text text-anchor="middle" dominant-baseline="middle" transform="rotate(-' + rotate + ' ' + circle_l_x + ' ' + circle_l_y +')" x="' + circle_l_x + '" y="' + circle_l_y + '" dy="0" font-size="' + $('#label')[0].value + '" font-family="sans-serif" fill="white">' + l + '</text>')
+        )
+
+      } else {
+        var [circle_l_x, circle_l_y] = [(l-0.5) * node_distance_x, -(arrow_start + arrow_thickness * 2)]
+        svg_core.append(
+          $('<text text-anchor="middle" dominant-baseline="middle" x="' + circle_l_x + '" y="' + circle_l_y + '" dy="0" font-size="' + $('#label')[0].value + '" font-family="sans-serif" fill="white">' + l + '</text>')
+        )
+        
+      }
+
+      l += k
+    };
+  }
+
+  for(var i in edges) {
+
+    var edge = data['elements']['edges'][i];
+    var edge_genomes = Object.keys(edge['genome'])
+
+    var intersection = edge_genomes.filter(x => enabled.includes(x));
+    if (intersection.length > 0) {
+      var edge_genomes_length = edge_genomes.length;
+
+      var color = pickcolor (edgecoloring, Object.keys(edge['genome']))
+
+      if (saturation == 1){
+        var pick = lighter_color('#ffffff', color, edge_genomes_length / genome_size);
+      } else {
+        var pick = color;
+      }
+
+      var source = edge['source']
+      var target = edge['target']
+
+      if (source != 'start' && target != 'stop' && edge['shown'] == 1){
+
+        var i_x = nodes[source]['position']['x_offset']
+        var i_y = nodes[source]['position']['y']
+        var j_x = nodes[target]['position']['x_offset']
+        var j_y = nodes[target]['position']['y']
+
+        for (let e = 0; e <= genomes.length; e++) {
+
+          if (e == genomes.length || (genomes[e] + 'layer' in middle_layers && edge_genomes.includes(genomes[e])) ) {
+
+            if (e == genomes.length) {
+
+              if (edge['direction'] == 'L') {
+                var stroke = ' stroke-dasharray="' + line_thickness * 5 + ',' + line_thickness * 5 + '" '
+              } else if (edge['direction'] == 'B') {
+                var stroke = ' stroke-dasharray="' + line_thickness * 20 + ',' + line_thickness * 5 + '" '
+              } else {
+                var stroke = ''
+              }
+
+              var [graph_size, graph_start, graph_stop] = outer_layers['graph']
+              var i_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + i_y * node_distance_y
+              var j_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + j_y * node_distance_y
+              var draw = pick
+              var thickness = edge_thickness
+            } else {
+              var [layer_width, layer_start, layer_stop] = middle_layers[genomes[e] + 'layer']
+
+              if (layer_width < line_thickness) {
+                var draw = ''
+              } else {
+                layer_width -= line_thickness
+                layer_start += line_thickness * 0.5
+                layer_stop -= line_thickness * 0.5
+
+                var i_y_size = layer_start + (i_y + 0.5) * (layer_width / global_y)
+                var j_y_size = layer_start + (j_y + 0.5) * (layer_width / global_y)
+                var draw = edgecoloring[genomes[e]][1]
+                var thickness = line_thickness
+                var stroke = ''
+              }
+            }
+
+            if (linear == 0){
+              var [circle_i_x, circle_i_y] = transform(i_x-0.5, i_y_size, theta);
+              var [circle_j_x, circle_j_y] = transform(j_x-0.5, j_y_size, theta);
+            } else {
+              var [circle_i_x, circle_i_y] = [(i_x-0.5) * node_distance_x, -i_y_size];
+              var [circle_j_x, circle_j_y] = [(j_x-0.5) * node_distance_x, -j_y_size];
+            }
+
+            if (draw !== "") {
+
+              if (edge['bended'] == ""){
+
+                if (i_y == j_y) {
+                  svg_edges.push(
+                    $('<path class="path" d="M ' + circle_i_x + ' ' + circle_i_y + ' A ' + i_y_size  + ' ' + j_y_size + ' 0 0 0 ' + circle_j_x + ' ' + circle_j_y + '"' + stroke + ' stroke="' + draw + '" stroke-width="' + thickness + '" fill="none"/>')
+                  )  
+                } else {
+                  svg_edges.push(
+                    $('<path class="path" d="M ' + circle_i_x + ' ' + circle_i_y + ' L ' + circle_j_x + ' ' + circle_j_y + '"' + stroke + ' stroke="' + draw + '" stroke-width="' + thickness + '" fill="none"/>')
+                  )
+                }
+
+
+              } else {
+
+                var bended_edge = '<path class="path" d="M ' + circle_i_x + ' ' + circle_i_y
+                var o_y = i_y
+
+                for(var n in edge['bended']) {
+
+                  var n_x = edge['bended'][n]['x']
+                  var n_y = edge['bended'][n]['y']
+
+                  if (e == genomes.length) {
+                    var o_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + o_y * node_distance_y
+                    var n_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + n_y * node_distance_y
+                  } else {
+                    var o_y_size = layer_start + (o_y + 0.5) * (layer_width / global_y)
+                    var n_y_size = layer_start + (n_y + 0.5) * (layer_width / global_y)
+                  }
+                  
+                  if (linear == 0){
+                    var [circle_n_x, circle_n_y] = transform(n_x-0.5, n_y_size, theta);
+                  } else {
+                    var [circle_n_x, circle_n_y] = [(n_x-0.5) * node_distance_x, -n_y_size];
+                  }
+
+                  if (o_y == n_y) {
+                    if (linear == 0){
+                      bended_edge += 'A ' + o_y_size  + ' ' + n_y_size + ' 0 0 0 ' + circle_n_x + ' ' + circle_n_y
+                    } else {
+                      bended_edge += 'L ' + circle_n_x + ' ' + circle_n_y
+                    }
+                  } else {
+                    bended_edge += 'L ' + circle_n_x + ' ' + circle_n_y
+                  }
+          
+                  var o_y = n_y
+                }
+
+                if (o_y == j_y) {
+                  if (linear == 0){
+                    bended_edge += 'A ' + o_y_size  + ' ' + j_y_size + ' 0 0 0 ' + circle_j_x + ' ' + circle_j_y + '"' + stroke + ' stroke="' + draw + '" stroke-width="' + thickness + '" fill="none"/>'
+                  } else {
+                    bended_edge += 'L ' + circle_j_x + ' ' + circle_j_y + '"' + stroke + ' stroke="' + draw + '" stroke-width="' + thickness + '" fill="none"/>'
+                  }
+                } else {
+                  bended_edge += 'L ' + circle_j_x + ' ' + circle_j_y + '"' + stroke + ' stroke="' + draw + '" stroke-width="' + thickness + '" fill="none"/>'
+                }
+
+                svg_edges.push(
+                  $(bended_edge)
+                )
+              }
+            }
+          }
+        }
+      }
+    }
+  };
+
+  var group_nodes = [];
+  var group_dict = {}
+  for(var g in groups) {
+    var group = data['infos']['groups'][g]
+
+    for (var node of group) {
+      group_dict[node] = g
+    }
+  };
+  group_nodes = Object.keys(group_dict)
+
+  var global_values = []
+  for(var k in nodes) {
+
+    if (k !=  'start' && k != 'stop') {
+
+      var node = data['elements']['nodes'][k];
+      var node_genomes = Object.keys(node['genome']);
+
+      var intersection = node_genomes.filter(x => enabled.includes(x));
+      if (intersection.length > 0) {
+
+        var node_genomes_length = node_genomes.length
+        
+        var k_x = parseInt(node['position']['x_offset'])
+        var k_y = parseInt(node['position']['y'])
+
+        if (!group_nodes.includes(k)) {
+          var node_class = 'class="node'
+
+          var x_value_start = parseInt(k_x) - 1
+          var x_value_stop = parseInt(k_x)
+
+        } else {
+          var node_class = 'stroke-opacity="0" fill-opacity="0" class="pseudo'
+          var g = group_dict[k]
+
+          var group = data['infos']['groups'][g]
+          var group_size = group.length
+          var group_compress = $('#groupcompress')[0].value
+          var group_size_compressed = Math.round(group_size * group_compress)
+
+          if (group_size_compressed == 0) {
+            group_size_compressed = 1
+          }
+          
+          var z_x = parseInt(data['elements']['nodes'][group[0]]['position']['x_offset'])
+
+          var fraction = group_size_compressed / (group_size)
+          var group_id = group.findIndex(x => x === k)
+
+          var x_value_start = parseInt(z_x) - (1 - group_id * fraction)
+          var x_value_stop = parseInt(z_x) - (1 - (group_id + 1) * fraction)
+
+        }
+
+        var color = pickcolor (edgecoloring, Object.keys(node['genome']))
+
+        if (saturation == 1) {
+          var draw = lighter_color('#ffffff', color, node_genomes_length / genome_size);
+          var draw2 = lighter_color('#ffffff', node_color, node_genomes_length / genome_size)
+        } else {
+          var draw = color;
+          var draw2 = node_color
+        }
+        
+        var [graph_size, graph_start, graph_stop] = outer_layers['graph']
+        var k_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + k_y * node_distance_y
+        
+        if (linear == 0) {
+          var [circle_k_x, circle_k_y] = transform(k_x-0.5, k_y_size, theta);
+        } else {
+          var [circle_k_x, circle_k_y] = [(k_x-0.5) * node_distance_x, -k_y_size];
+        }
+
+        svg_nodes.push(
+          $('<circle ' + node_class + '" id="' + k + '" cx="' + circle_k_x + '" cy="' + circle_k_y + '" r="' + node_size + '" fill="' + draw2 + '" stroke="' + draw + '" stroke-width="' + node_thickness + '"/>')
+        )
+
+        var add_start = 1
+        var add_stop = 0
+
+        var [search_size, search_start, search_stop] = middle_layers['search']
+        
+        var i_x = parseInt(k_x)-add_start
+        var i_y = search_start
+        var j_x = parseInt(k_x)+add_stop
+        var j_y = search_stop
+
+        if (!global_values.includes(k_x)) {
+          svg_search.push(create_rectangle(i_x, i_y, j_x, j_y, theta, node_distance_x, linear, 'none', k_x))
+        }
+
+        for (var layer_name of layers) {
+
+          if ($('#flex' + layer_name).prop('checked') == true){
+
+            var value = node['layer'][layer_name]
+            var max = data['infos']['layers_data'][layer_name]['max']
+
+            var [layer_width, layer_start, layer_stop] = outer_layers[layer_name]
+            var k_y_size = sum_middle_layer + k_y * node_distance_y
+
+            var i_x = x_value_start
+            var i_y = layer_start + k_y_size
+            var j_x = x_value_stop
+            var j_y = layer_stop + k_y_size
+            var color = lighter_color('#00ff00', '#ff0000', value / max)
+
+            svg_heatmaps.push(create_rectangle(i_x, i_y, j_x, j_y, theta, node_distance_x, linear, color))
+          }
+        }
+      }
+    }
+
+    global_values.push(k_x)
+
+  };
+
+  for(var l in groups) {
+
+    var group = data['infos']['groups'][l]
+    
+    var group_length = group.length
+    var left_node_name = group[0]
+    var right_node_name = group[group_length-1]
+
+    var left_node = data['elements']['nodes'][left_node_name];
+    var right_node = data['elements']['nodes'][right_node_name];
+
+    var group_genomes = Object.keys(left_node['genome']);
+    var intersection = group_genomes.filter(x => enabled.includes(x));
+    if (intersection.length > 0) {
+
+      var group_genomes_length = group_genomes.length;
+
+      var color = pickcolor (edgecoloring, Object.keys(left_node['genome']))
+      
+      if (saturation == 1) {
+        var draw = lighter_color('#ffffff', color, group_genomes_length / genome_size);
+      } else {
+        var draw = color;
+      }
+      
+      var l_x = parseInt(left_node['position']['x_offset'])
+      var l_y = parseInt(left_node['position']['y'])
+
+      var m_x = parseInt(right_node['position']['x_offset'])
+      var m_y = parseInt(right_node['position']['y'])
+
+      var [graph_size, graph_start, graph_stop] = outer_layers['graph']
+      var l_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + l_y * node_distance_y
+      var m_y_size = sum_middle_layer + graph_start + graph_size * 0.5 + m_y * node_distance_y
+
+      var i_x = l_x-0.5
+      var i_y = l_y_size + node_size
+      var j_x = m_x-0.5
+      var j_y = m_y_size - node_size
+
+      if (saturation == 1) {
+        var color = lighter_color('#ffffff', group_color, group_genomes_length / genome_size)
+      } else {
+        var color = group_color
+      }
+
+      if ((l_x - m_x) * theta >= 180) {
+        var arc_flag = 1
+      } else {
+        var arc_flag = 0
+      }
+    
+      if (linear == 0) {
+        var [a_x, a_y] = transform(i_x, i_y, theta)
+        var [b_x, b_y] = transform(i_x, j_y, theta)
+        var [c_x, c_y] = transform(j_x, i_y, theta)
+        var [d_x, d_y] = transform(j_x, j_y, theta)
+    
+        var path = $('<path class="group" id="' + l + '" d="' +
+        'M ' + a_x + ' ' + a_y + ' ' +
+        'A ' + (l_y_size + node_size) + ' ' + (l_y_size + node_size) + ' 0 ' + arc_flag + ' 0 ' + c_x + ' ' + c_y + ' ' +
+        'A ' + node_size + ' ' + node_size + ' 0 0 0 ' + d_x + ' ' + d_y + ' ' +
+        'A ' + (m_y_size - node_size) + ' ' + (m_y_size - node_size) + ' 0 ' + arc_flag + ' 1 ' + b_x + ' ' + b_y + ' ' +
+        'A ' + node_size + ' ' + node_size + ' 0 0 0 ' + a_x + ' ' + a_y +
+        '" fill="' + color + '" stroke="' + draw + '" stroke-width="' + node_thickness + '"/>')
+    
+      } else {
+        var [a_x, a_y] = [i_x * node_distance_x, -i_y]
+        var [b_x, b_y] = [i_x * node_distance_x, -j_y]
+        var [c_x, c_y] = [j_x * node_distance_x, -i_y]
+        var [d_x, d_y] = [j_x * node_distance_x, -j_y]
+    
+        var path = $('<path class="group" id="' + l + '" d="' +
+        'M ' + a_x + ' ' + a_y + ' ' +
+        'L ' + c_x + ' ' + c_y + ' ' +
+        'A ' + node_size + ' ' + node_size + ' 0 0 1 ' + d_x + ' ' + d_y + ' ' +
+        'L ' + b_x + ' ' + b_y + ' ' +
+        'A ' + node_size + ' ' + node_size + ' 0 0 1 ' + a_x + ' ' + a_y +
+        '" fill="' + color + '" stroke="' + draw + '" stroke-width="' + node_thickness + '"/>')
+      }
+
+      svg_groups.push(path)
+    }
+  };
+
+  for (var layer_name of layers) {
+
+    if ($('#flex' + layer_name).prop('checked') == true){
+      var [layer_width, layer_start, layer_stop] = outer_layers[layer_name]
+      var y_size = sum_middle_layer + layer_width * 0.5
+      
+      if (linear == 0){
+        var [circle_x, circle_y] = transform(0, (layer_start + y_size), theta)
+      } else {
+        var [circle_x, circle_y] = [0, -(layer_start + y_size)]
+      }
+
+      svg_heatmaps.push(
+        $('<text text-anchor="end" transform="translate (-10)" dominant-baseline="middle" x="' + circle_x + '" y="' + circle_y + '" dy="0" font-size="' + $('#label')[0].value + '" font-family="sans-serif" fill="black">' + layer_name + '</text>')
+      )
+    }
+  }
+
+  item_dist = {}
+  for (var genome_name of item_order) {
+    if ($('#flex' + genome_name + 'layer').prop('checked') == true){
+      var [layer_width, layer_start, layer_stop] = middle_layers[genome_name + 'layer']
+      
+      if (layer_width >= edge_thickness) {
+      
+        var y_size = layer_start + layer_width * 0.5
+
+        if (linear == 0){
+          var [circle_x, circle_y] = transform(0, y_size, theta)
+        } else {
+          var [circle_x, circle_y] = [0, -y_size]
+        }
+
+        item_dist[genome_name] = circle_y
+
+        svg_edges.push(
+          $('<text text-anchor="end" transform="translate (-10)" dominant-baseline="middle" x="' + circle_x + '" y="' + circle_y + '" dy="0" font-size="' + $('#label')[0].value + '" font-family="sans-serif" fill="black">' + genome_name + '</text>')
+        )
+      }
+    }
+  }
+
+  // tree_length
+  // console.log(Object.keys(item_dist).length, item_order.length)
+
+  if ($('#flextree').prop('checked') == true){
+    svg_core.append(draw_newick(order, item_dist, max_dist, offset, tree_length, tree_thickness))
+  }
+
+  for (var item of svg_search) svg_core.append(item);
+  for (var item of svg_heatmaps) svg_core.append(item);
+  for (var item of svg_edges) svg_core.append(item);
+  for (var item of svg_nodes) svg_core.append(item);
+  for (var item of svg_groups) svg_core.append(item);
+
+  body.append(svg_core)
+  body.html(body.html());
+}
+
+//ANCHOR - Check node
+async function checknode(searchfunction) {
+
+  var keys = Object.keys(searchfunction)  
+  if (keys.length > 0) {
+    var d = await get_passed_gene_clusters(searchfunction)
+    var result = d['gene_clusters']
+  } else {
+    var result = []
+  }
+
+  return result
+}
+
+function main () {
+
+  $.ajax({
+    url: "/pangraph/get_json",
+    type: "POST",
+    cache: false,
+    //data: JSON.stringify(data),
+    contentType: "application/json",
+    dataType: "json",
+    success: function(data){
+
+    var layers = Object.keys(data['infos']['layers_data'])
+  
+    for (var layer_name of layers) {
+      
+      var layer_scale = data['infos']['layers_data'][layer_name]['scale']
+
+      if (layer_scale == 'global') {
+        var value = '50'
+      } else {
+        var value = '10'
+      }
+    
+      if ($('#flex' + layer_name + '').length > 0) {
+        // console.log(layer_name)
+      } else {
+        var element = $('<div class="col-12 d-flex mb-1"></div>').append(
+          $('<div class="col-2 d-flex align-items-center"></div>').append(
+            $('<div class="form-switch d-flex"></div>').append(
+              $('<input class="" type="checkbox" id="flex' + layer_name + '" name="flex' + layer_name + '" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+            )
+          )
+        ).append(
+            $('<div class="col-8 d-flex align-items-center"></div>').append(
+              layer_name
+            )
+        ).append(
+          $('<div class="d-flex col-2"></div>').append(
+            $('<input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="' + layer_name + '" name="' + layer_name + '" value=' + value + ' aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">')
+          )
+        )
+
+        $('#layers').append(element)
+      }
+
+    }
+
+    // This title must update with Generic data from JSON
+    $('#title-panel-first-line').text(data['infos']['meta']['title']);
+    $('#title-panel-second-line').text('Pangraph Detail');
+
+    // It seems unused function after UI changes
+    $('#redraw').on('click', function() {
+
+      var data = new Object;
+
+      data['condtr'] = parseInt($('#condtr')[0].value)
+      data['maxlength'] = parseInt($('#maxlength')[0].value)
+      data['groupcompress'] = parseFloat($('#groupcompress')[0].value)
+      data['ungroup'] = [parseInt($('#ungroupfrom')[0].value), parseInt($('#ungroupto')[0].value)]
+
+      $("#genomecolors :input[type='checkbox']").each((index, element) => {
+
+        var genome = $(element).attr('name')
+        if ($(element).prop('checked') == true){
+          data[genome] = 'on'
+        } else {
+          data[genome] = 'off'
+        }
+      })
+
+      $.ajax({
+          url: "/pangraph/settings",
+          type: "POST",
+          async: false,
+          data: JSON.stringify(data),
+          contentType: "application/json",
+          dataType: "json",
+          success: function(){
+            $(document).off("click", ".group_choice");
+            $(document).off("click", ".binremove");
+            $(document).off("click", ".binchoice li a");
+            $(document).off("change", ".colorchange");
+            $(document).find("*").off();
+            main()
+          }
+      });
+    })
+
+    $("#condtr")[0].value = data['infos']['gene_cluster_grouping_threshold']
+    $("#maxlength")[0].value = data['infos']['max_edge_length_filter']
+    $("#groupcompress")[0].value = data['infos']['groupcompress']
+    $("#ungroupfrom")[0].value = data['infos']['ungroup'][0]
+    $("#ungroupto")[0].value = data['infos']['ungroup'][1]
+
+    if (!$('#genomecolors').children().length) {
+
+      for (var [genome, value] of Object.entries(data['infos']['genomes'])) {
+
+        var state = ''
+        if (value == 'on') {
+          state = ' checked'
+        }
+
+        $('#genomecolors').append(
+          $('<div class="col-12 d-flex mb-1">').append(
+              $('<div class="col-2 d-flex align-items-center">').append(
+                $('<div class="form-switch d-flex">').append(
+                  $('<input class="" type="checkbox" id="flex' + genome + '" name="' + genome + '" aria-label="..." data-bs-toggle="tooltip" data-bs-placement="top" title="Tooltip on top"' + state + '>')
+                )
+              )
+            ).append(
+              $('<div class="col-7 d-flex align-items-center">').append(
+                genome
+              )
+            ).append(
+              $('<div class="col-1 d-flex align-items-center">').append(
+                $('<i class="user-handle bi bi-arrows-expand"></i>')
+              )
+            ).append(
+              $('<div class="d-flex col-2">').append(
+                $('<input type="color" class="form-control form-control-color flex-fill p-0 border-0" id="' + genome + '" name="' + genome + '" aria-label="..." data-bs-toggle="tooltip" data-bs-placement="top" title="Choose your color">')
+              )
+            )
+          )
+        // )
+
+        $('#RightOffcanvasBodyTop').append(
+          $('<tr>').append(
+            $('<td class="col-8">').append(
+              genome
+            )
+            ).append(
+              $('<td class="col-4 text-end" id="number_' + genome + '">').append(
+                0
+              )
+          )
+        )
+
+        if ($('#flex' + genome + 'layer').length > 0) {
+          // console.log(layer_name)
+        } else {
+          var element = $('<div class="col-12 d-flex mb-1"></div>').append(
+            $('<div class="col-2 d-flex align-items-center"></div>').append(
+              $('<div class="form-switch d-flex"></div>').append(
+                $('<input class="" type="checkbox" id="flex' + genome + 'layer" name="flex' + genome + 'layer" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+              )
+            )
+          ).append(
+              $('<div class="col-8 d-flex align-items-center"></div>').append(
+                genome
+              )
+          ).append(
+            $('<div class="d-flex col-2"></div>').append(
+              $('<input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="' + genome + 'layer" name="' + genome + 'layer" value=50 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">')
+            )
+          )
+
+          $('#layers').append(element)
+        }
+      }
+    }
+
+    var body = $('#svgbox')
+    body.empty()
+
+    // learn about the functional annotation sources
+    functional_annotation_sources_available = data['infos']['functional_annotation_sources_available'];
+    $('#searchSources').empty()
+    for (var annotation_source of functional_annotation_sources_available){
+      $('#searchSources').append(
+        $('<div class="col-12"></div>').append(
+          $('<div class="row align-items-center"></div>').append(
+            $('<div class="col-2 mb-1"></div>').append(
+              $('<input class="" type="checkbox" id="flex' + annotation_source + '" value="" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+            )
+          ).append(  
+            $('<div class="col-8 mb-1"></div>').append(
+              annotation_source
+            )
+          ).append(
+            $('<div class="col-2 mb-1"></div>')
+          )
+        )
+      )
+    }
+
+    var layers = Object.keys(data['infos']['layers_data'])
+
+    $('#expressiondrop').empty()
+    $('#expressiondrop').append($('<option value="Choose item">Choose item</option>'))
+    $('#expressiondrop').append($('<option value="Name">Name</option>'))
+    $('#expressiondrop').append($('<option value="Position">Position</option>'))
+
+    $('#filter').empty()
+    $('#filter').append(
+      $('<div class="col-12"></div>').append(
+        $('<div class="row align-items-center"></div>').append(
+          $('<div class="col-2 mb-1"></div>').append(
+            $('<input class="" type="checkbox" id="minposition" value="" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+          )
+        ).append(  
+          $('<div class="col-8 mb-1"></div>').append(
+            'Min graph position'
+          )
+        ).append(
+          $('<div class="col-2 mb-1"></div>').append(
+            $('<input type="text" class="form-control flex-fill p-0 border-0" style= "background-color: #e9ecef;" value="" id="minpositiontext" aria-describedby="">')
+          )  
+        ).append(
+          $('<div class="col-2 mb-1"></div>').append(
+            $('<input class="" type="checkbox" id="maxposition" value="" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+          )
+        ).append( 
+          $('<div class="col-8 mb-1"></div>').append(
+            'Max graph position' 
+          )
+        ).append(
+          $('<div class="col-2 mb-1"></div>').append(
+            $('<input type="text" class="form-control flex-fill p-0 border-0" style= "background-color: #e9ecef;" value="" id="maxpositiontext" aria-describedby="">')
+          )
+        )
+      )
+    )
+
+    for (var layer_name of layers) {
+      if ($('#flex' + layer_name).prop('checked') == true){
+
+        $('#expressiondrop').append($('<option value="' + layer_name + '">' + layer_name + '</option>'))
+        $('#filter').append(
+          $('<div class="col-12"></div>').append(
+            $('<div class="row align-items-center"></div>').append(
+              $('<div class="col-2 mb-1"></div>').append(
+                $('<input class="" type="checkbox" id="min' + layer_name + '" value="" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+              )
+            ).append(  
+              $('<div class="col-8 mb-1"></div>').append(
+                'Min ' + layer_name
+              )
+            ).append(
+              $('<div class="col-2 mb-1"></div>').append(
+                $('<input type="text" class="form-control flex-fill p-0 border-0" style= "background-color: #e9ecef;" value="" id="min' + layer_name + 'text" aria-describedby="">')
+              )  
+            ).append(
+              $('<div class="col-2 mb-1"></div>').append(
+                $('<input class="" type="checkbox" id="max' + layer_name + '" value="" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">')
+              )
+            ).append( 
+              $('<div class="col-8 mb-1"></div>').append(
+                'Max ' + layer_name
+              )
+            ).append(
+              $('<div class="col-2 mb-1"></div>').append(
+                $('<input type="text" class="form-control flex-fill p-0 border-0" style= "background-color: #e9ecef;" value="" id="max' + layer_name + 'text" aria-describedby="">')
+              )
+            )
+          )
+        )
+      }
+    }
+
+    generate_svg(body, data);
+
+    window.zoomSVG = svgPanZoom('#result', {
+      zoomEnabled: true,
+      panEnabled: false,
+      controlIconsEnabled: false,
+      minZoom: 0.1,
+      maxZoom: 100
+    });
+
+    //ANCHOR - Zoom pan functions
+    // $('#plus').on('click', function() {
+    //   window.zoomSVG.zoomIn();
+    // })
+
+    // $('#minus').on('click', function() {
+    //   window.zoomSVG.zoomOut();
+    // })
+
+    $('#fit').on('click', function() {
+      window.zoomSVG.resize();
+      window.zoomSVG.fit();
+      window.zoomSVG.center();
+    })
+
+    //ANCHOR - Main panel response functions
+
+    
+    
+    if ($('#condtr')[0].value == -1){
+      // $('#customRange2').prop('disabled', true);
+      $('#flexcondtr').prop('checked', false);
+    }
+
+    if ($('#maxlength')[0].value == -1){
+      // $('#customRange3').prop('disabled', true);
+      $('#flexmaxlength').prop('checked', false);
+    }
+
+    if ($('#groupcompress')[0].value == -1){
+      $('#flexgroupcompress').prop('checked', false);
+    }
+
+    $('#flexcondtr').change(function() {
+      if ($(this).prop('checked') == true){
+        $('#condtr')[0].value = 2;
+        $('#condtr').prop('disabled', false)
+        // $('#customRange2')[0].value = 2;
+        // $('#customRange2').prop('disabled', false);
+      } else {
+        $('#condtr')[0].value = -1;
+        $('#condtr').prop('disabled', true)
+        // $('#customRange2')[0].value = 2;
+        // $('#customRange2').prop('disabled', true);
+      }
+    })
+
+    $('#flexmaxlength').change(function() {
+      if ($(this).prop('checked') == true){
+        $('#maxlength')[0].value = 1;
+        $('#maxlength').prop('disabled', false)
+        // $('#customRange3')[0].value = 1;
+        // $('#customRange3').prop('disabled', false);
+      } else {
+        $('#maxlength')[0].value = -1;
+        $('#maxlength').prop('disabled', true)
+        // $('#customRange3')[0].value = 1;
+        // $('#customRange3').prop('disabled', true);
+      }
+    })
+
+    $('#flexgroupcompress').change(function() {
+      if ($(this).prop('checked') == true){
+        $('#groupcompress')[0].value = 0.0;
+        $('#groupcompress').prop('disabled', false)
+        // $('#customRange4')[0].value = 0;
+        // $('#customRange4').prop('disabled', false);
+      } else {
+        $('#groupcompress')[0].value = 1.0;
+        $('#groupcompress').prop('disabled', true)
+        // $('#customRange4')[0].value = 0;
+        // $('#customRange4').prop('disabled', true);
+      }
+    })
+
+    $('#flexungroup').change(function() {
+      if ($(this).prop('checked') == true){
+        $('#ungroupfrom')[0].value = 0;
+        $('#ungroupfrom').prop('disabled', false)
+        $('#ungroupto')[0].value = 0;
+        $('#ungroupto').prop('disabled', false)
+      } else {
+        $('#ungroupfrom')[0].value = -1;
+        $('#ungroupfrom').prop('disabled', true)
+        $('#ungroupto')[0].value = -1;
+        $('#ungroupto').prop('disabled', true)
+      }
+    })
+
+    $('#flextree').change(function() {
+      if ($(this).prop('checked') == true){
+        var genomes = Object.keys(data["infos"]["genomes"])
+        for (var genome of genomes) {
+          $('#flex' + genome + 'layer').prop('checked', true);
+          $('#flex' + genome + 'layer').prop('disabled', true);
+        }
+      } else {
+        var genomes = Object.keys(data["infos"]["genomes"])
+        for (var genome of genomes) {
+          $('#flex' + genome + 'layer').prop('disabled', false);
+        }
+      }
+    })
+
+    sortable('#genomecolors', {
+      forcePlaceholderSize: true,
+      handle: '.user-handle',
+      items: 'div'
+    });
+
+    $(document).on("click", ".group_choice", async function() {
+
+      // console.log(this)
+
+      var gene_cluster_id = this.getAttribute("name_id");
+      var gene_cluster_context = this.getAttribute("group");
+      var add_align = parseInt(this.getAttribute("context"))
+
+      var body = $(this).parent().parent().parent().parent()
+
+      body.empty()
+      var bodyinfo = $('<div class="card-body overflow-scroll"></div>')
+      body.append(bodyinfo)
+
+      // console.log(gene_cluster_id, gene_cluster_context)
+
+      var all_info = await get_gene_cluster_display_tables(gene_cluster_id, gene_cluster_context, data, add_align)
+
+      // console.log(all_info)
+
+      bodyinfo.append(all_info)
+      // nodeinfo(e.target, data);
+    })
+
+    //ANCHOR - Recolor nodes after redraw
+    var groups = data['infos']['groups']
+    for (var binid of Object.keys(bins)) {
+      var nodes = bins[binid];
+      var updated_nodes = []
+
+      for (var node of nodes) {
+
+        var name = document.getElementById(node);
+
+        if(name) {
+          if (name.getAttribute('class') == 'pseudo') {
+            for(var g in groups) {
+              var group = data['infos']['groups'][g]
+              if (group.includes(node)) {
+                if (!updated_nodes.includes(g)){
+                  updated_nodes.push(g)
+                }
+              }
+            }
+          } else {
+            updated_nodes.push(node)
+          }
+        } else {
+          updated_nodes.push(...current_groups[node])
+        };
+
+      }
+
+      bins[binid] = updated_nodes
+      // console.log(nodes)
+      // console.log(updated_nodes)
+      for (var node of bins[binid]) {
+
+        bins[binid] = bins[binid].filter(item => item !== node);
+        var name = document.getElementById(node);
+        bins = marknode(name, data, binid, bins);
+
+      }
+    }
+
+    // console.log(bins)
+
+    current_groups = data['infos']['groups']
+
+    // console.log(current_groups)
+
+    //ANCHOR - Bin dropdown choice function
+    $(document).on("click", ".binremove", function() {
+
+      var id = $(this).attr('name_id');
+      var binid = $(this).attr('bin');
+
+      var name = document.getElementById(id);
+      // console.log(name)
+      bins = marknode(name, data, binid, bins);
+
+      $(this).parent().parent().parent().remove();
+
+      // console.log(bins)
+
+    })
+    
+    // ANCHOR - Add bin
+    $('#binadd').on('click', function() {
+        binnum += 1;
+    
+        $('#bingrid').append(
+            $('<div class="col-12" id="bin' + binnum + '"></div>').append(
+                $('<div class="row gy-1 align-items-center" id="row' + binnum + '"></div>').append(
+                    $('<div class="col-2"></div>').append(
+                        $('<input type="radio" name="binradio" id="bin' + binnum + 'radio" value="bin' + binnum + '" checked></input>')
+                    )
+                ).append(
+                    $('<div class="col-6"></div>').append(
+                        $('<input class="form-control flex-fill p-0 border-0" style="background-color: #e9ecef;" type="text" id="bin' + binnum + 'text" value="Bin_' + binnum + '"></input>')
+                    )
+                ).append(
+                    $('<div class="col-2"></div>').append(
+                        $('<input type="text" class="form-control float-end text-end flex-fill p-0 border-0" id="bin' + binnum + 'value" name="condtr" value="0" readonly>')
+                    )
+                ).append(
+                    $('<div class="d-flex col-2"></div>').append(
+                        $('<input class="form-control form-control-color flex-fill p-0 border-0 colorchange" type="color" name="bin' + binnum + '" id="bin' + binnum + 'color" value="#000000"></input>')
+                    )
+                )
+            )
+        );
+    
+        bins['bin' + binnum] = [];
+    });
+    
+    $('#AddBin').on('click', function() {
+
+      var selection = document.querySelector('input[name="binradio"]:checked');
+      var binid = selection.value;
+
+      var basics = $('#node_basics_table')
+      var node = basics[0].getAttribute("gc_context")
+      var name = document.getElementById(node);
+
+      bins = marknode(name, data, binid, bins);
+
+    });
+
+    //ANCHOR - Remove bin
+    $('#binremove').on('click', function() {
+
+      var selection = document.querySelector('input[name="binradio"]:checked');
+
+      if (selection !== null) {
+        var binid = selection.value;
+
+        for (var node of bins[binid]) {
+          var name = document.getElementById(node);
+          bins = marknode(name, data, binid, bins);
+        }
+
+        $("#" + binid).remove();
+        delete bins[binid]
+        var nextbin = document.querySelector('input[name="binradio"]')
+
+        if (nextbin) {
+          nextbin.checked = true;
+        } else {
+          $('#binadd').click();
+        }
+      }
+    })
+
+    //ANCHOR - Change bin
+    $(document).on("change", ".colorchange", function() {
+
+      var binid = this.name;
+      var nodes = bins[binid];
+
+      for (var node of nodes) {
+
+        bins[binid] = bins[binid].filter(item => item !== node);
+        var name = document.getElementById(node);
+        bins = marknode(name, data, binid, bins);
+
+      }
+
+    });
+
+    $('#binanalyse').on('click', async function() {
+      var set = {}
+      var groups = data['infos']['groups']
+      var groups_keys = Object.keys(groups)
+      var bin_keys = Object.keys(bins)
+
+      var selection = 'COG20_FUNCTION'
+      set['selection'] = selection
+      // console.log(bins, bin_keys)
+
+      for (var binid of bin_keys) {
+        set[binid] = []
+        for (var id of bins[binid]) {
+          if (groups_keys.includes(id)) {
+            for (var item of groups[id]) {
+              set[binid].push(data['elements']['nodes'][item]['name'])  
+            }
+          } else {
+            set[binid].push(data['elements']['nodes'][id]['name'])
+          }
+        }
+      }
+
+      $.ajax({
+        url: "/pangraph/analyse",
+        type: "POST",
+        data: JSON.stringify(set),
+        contentType: "application/json",
+        dataType: "json",
+        success: function(result){
+          
+          $('#BinAnalyseBody').empty();
+          var bin_analyses_table = ''
+
+          bin_analyses_table += '<table class="table'
+          bin_analyses_table += '<tbody><thead class="thead-light"><tr>'
+          
+          bin_analyses_table += '<th scope="row">' + 'Function' + '</th>'
+          for (bin_key of bin_keys) {
+            bin_analyses_table += '<th scope="row">' + bin_key + '</th>'
+          }
+          
+          bin_analyses_table += '</tr></thead><tbody>'
+          bin_analyses_table += '<tbody>'
+
+          for (func of Object.keys(result)) {
+            bin_analyses_table += '<tr><td>' + func + '</td>'
+            for (bin_key of Object.keys(result[func])) {
+              var value = result[func][bin_key]
+              if (value == 1) {
+                bin_analyses_table += '<td class=td-analysis-cell-1></td>'
+              } else {
+                bin_analyses_table += '<td class=td-analysis-cell-0></td>'
+              }
+            }
+            bin_analyses_table += '</tr>'
+          }
+
+          bin_analyses_table += '</tbody></table>'
+
+          $('#BinAnalyseBody')[0].innerHTML = bin_analyses_table
+
+          $('#BinAnalyse').modal('show');
+
+        }
+      })
+      // console.log(set)
+    })
+
+    //ANCHOR - Info bin
+    $('#bininfo').on('click', async function() {
+
+      var selection = document.querySelector('input[name="binradio"]:checked');
+
+      // if (selection !== null) {
+      var binid = selection.value;
+      var appendlist = [];
+
+      $('#BinModalBody').empty();
+      for (var id of bins[binid]) {
+        var element = document.getElementById(id);
+
+        if (element.getAttribute('class') == 'group') {
+          gene_cluster_context = id;
+          gene_cluster_id = data['infos']['groups'][id][0]
+        } else {
+          gene_cluster_id = id;
+          gene_cluster_context = null;
+        }
+
+        appendlist.push([gene_cluster_id, gene_cluster_context]);
+
+      }
+
+      for (var [gene_cluster_id, gene_cluster_context] of appendlist) {
+
+        var body = $('<div></div>').append(
+          $('<div class="card-body overflow-scroll" id="' + gene_cluster_id + 'div"></div>').append(
+            await get_gene_cluster_display_tables(gene_cluster_id, gene_cluster_context, data, add_align=0)
+          )
+        )
+
+        if (gene_cluster_context == null) {
+          var element_id = gene_cluster_id
+        } else {
+          var element_id = gene_cluster_context
+        }
+
+        $('#BinModalBody').append(
+          $('<div class="card border mb-3 w-100"></div>').append(
+            $('<div class="card-header"></div>').append(
+              $('<div class="d-flex justify-content-end align-items-center"></div>').append(
+                $('<button class="btn-close binremove" name_id="' + element_id + '" bin="' + binid + '"></button>')
+              )
+            )
+          ).append(
+            body
+          )
+        )
+
+        // basic_info = {'Gene Cluster': id, 'Genomes': genomes, 'Position': position}
+        // body.append(get_gene_cluster_display_tables(id, basic_info, gene_cluster_data))
+      }
+
+      $('#BinModal').modal('show');
+      // }
+    })
+
+    $('#InfoDownload').on('click', function() {
+
+      // Variable to store the final csv data
+      var csv_data = [];
+      var basics = $('#node_basics_table')
+      var title = basics[0].getAttribute("gc_id")
+      var layers = $('#node_layers_table')
+      var functions = $('#node_functions_table')
+
+      var basics_rows = basics[0].getElementsByTagName('tr');
+      var layers_rows = layers[0].getElementsByTagName('tr');
+      
+      var function_rows = functions[0].getElementsByTagName('tr');
+
+      for (let i = 0; i < function_rows.length; i++) {
+    
+          if (i >= basics_rows.length) {
+            var basics_cols = []
+            basics_cols = Array.prototype.concat.apply(basics_cols, basics_rows[1].querySelectorAll('td,th'));
+            basics_cols = Array.prototype.concat.apply(basics_cols, layers_rows[1].querySelectorAll('td,th'));
+            
+            var function_cols = function_rows[i].querySelectorAll('td,th');
+          } else { 
+            var basics_cols = []
+            basics_cols = Array.prototype.concat.apply(basics_cols, basics_rows[i].querySelectorAll('td,th'));
+            basics_cols = Array.prototype.concat.apply(basics_cols, layers_rows[i].querySelectorAll('td,th'));
+            
+            var function_cols = function_rows[i].querySelectorAll('td,th');
+          }
+            
+          let csvrow = [];
+          for (let j = 0; j < basics_cols.length; j++) {
+    
+            var info = basics_cols[j].innerHTML
+            csvrow.push(info);
+          }
+          
+          for (let k = 0; k < function_cols.length; k++) {
+    
+            var info = function_cols[k].innerHTML
+            csvrow.push(info);
+          }
+    
+          // console.log(csvrow)
+
+          // Combine each column value with comma
+          csv_data.push(csvrow.join(","));
+      }
+      // Combine each row data with new line character
+      csv_data = csv_data.join('\n');
+    
+      var blob = new Blob([csv_data]);
+      // var title = data['infos']['meta']['title']
+      downloadBlob(blob, title + ".csv");
+    });
+
+    $('#AlignmentDownload').on('click', function() {
+
+      // Variable to store the final csv data
+      var csv_data = '';
+      var alignment = $('#node_sequence_alignments_table')
+      var basics = $('#node_basics_table')
+      var title = alignment[0].getAttribute("gc_id")
+      var xpos = basics[0].getAttribute("gc_pos")
+      
+      var alignment_rows = alignment[0].getElementsByTagName('tr');
+
+      for (let i = 1; i < alignment_rows.length; i++) {
+    
+          var alignment_cols = alignment_rows[i].querySelectorAll('td,th');
+    
+          csv_data += ">" + title + "|Genome:" + alignment_cols[0].innerHTML +"|Genecall:" + alignment_cols[1].innerHTML + "|Contig:" + alignment_cols[2].innerHTML + "|Position:" + xpos + "|Direction:" + alignment_cols[3].innerHTML + '\n';
+          var genome = ''
+          
+          var alignment_nucs = alignment_cols[4].getElementsByTagName('span');
+          // console.log(alignment_nucs)
+
+          for (let k = 0; k < alignment_nucs.length; k++) {
+
+            genome += alignment_nucs[k].innerHTML
+          }
+
+          csv_data += genome.match(/.{1,60}/g).join("\r\n") + "\n"
+      }
+      // Combine each row data with new line character
+      
+      var blob = new Blob([csv_data]);
+      // var title = data['infos']['meta']['title']
+      downloadBlob(blob, title + ".fa");
+    });
+
+    $('#svgDownload').on('click', function() {
+      var blob = new Blob([$('#svgbox')[0].innerHTML]);
+      var title = data['infos']['meta']['title']
+      downloadBlob(blob, title + ".svg");
+    });
+
+    $('#searchadd').on('click', function() {
+
+      var selection = document.querySelector('input[name="binradio"]:checked')
+      var binid = selection.value
+
+      for (var [id, members] of Object.entries(searched)) {
+        if (!(bins[binid].includes(id))) {
+
+          var e = document.getElementById(id);
+          bins = marknode(e, data, binid, bins);
+
+        }
+      }
+    })
+
+    $('#searchremove').on('click', function() {
+
+      var selection = document.querySelector('input[name="binradio"]:checked')
+      var binid = selection.value
+
+      for (var [id, members] of Object.entries(searched)) {
+        if ((bins[binid].includes(id))) {
+
+          var e = document.getElementById(id);
+          bins = marknode(e, data, binid, bins);
+
+        }
+      }
+    })
+
+    $('#searcherase').on('click', function() {
+
+      for (var [id, members] of Object.entries(searched)) {
+        for (var mem of members) {
+          var xpos = data['elements']['nodes'][mem]['position']['x_offset']
+          var e = document.getElementById(xpos);
+          e.setAttribute("fill", "white")
+        }
+      }
+
+      searched = {};
+    })
+
+    $('#searchcolor').on('click', function() {
+
+      for (var [id, members] of Object.entries(searched)) {
+        for (var mem of members) {
+          var xpos = data['elements']['nodes'][mem]['position']['x_offset']
+          var e = document.getElementById(xpos);
+          e.setAttribute("fill", "#ff0000")
+        }
+      }
+    })
+
+    const searchEraseButton = document.getElementById('searcherase');
+    const searchColorButton = document.getElementById('searchcolor');
+    const searchAppendBin = document.getElementById('searchadd');
+    const searchRemoveBin = document.getElementById('searchremove');
+    
+    var searched = {}
+    $('#search').on('click', async function() {
+
+      var searchpos = false
+
+      //Filter Search
+      var layers_filter = new Object
+      var mingenomes = ($("#mingenomes").prop('checked') == true && !isNaN(parseFloat($("#mingenomestext")[0].value))) ? parseFloat($("#mingenomestext")[0].value) : -1
+      var maxgenomes = ($("#maxgenomes").prop('checked') == true && !isNaN(parseFloat($("#maxgenomestext")[0].value))) ? parseFloat($("#maxgenomestext")[0].value) : -1
+      var minposition = ($("#minposition").prop('checked') == true && !isNaN(parseFloat($("#minpositiontext")[0].value))) ? parseFloat($("#minpositiontext")[0].value) : -1
+      var maxposition = ($("#maxposition").prop('checked') == true && !isNaN(parseFloat($("#maxpositiontext")[0].value))) ? parseFloat($("#maxpositiontext")[0].value) : -1
+      
+      layers_filter['genomes'] = {'min': mingenomes, 'max': maxgenomes}
+      layers_filter['position'] = {'min': minposition, 'max': maxposition}
+
+      var layers = Object.keys(data['infos']['layers_data'])
+      for (var layer_name of layers) {
+
+        // console.log("#min" + layer_name + "text")
+        var minlayer = ($("#min" + layer_name).prop('checked') == true && !isNaN(parseFloat($("#min" + layer_name + "text")[0].value))) ? parseFloat($("#min" + layer_name + "text")[0].value) : -1
+        var maxlayer = ($("#max" + layer_name).prop('checked') == true && !isNaN(parseFloat($("#max" + layer_name + "text")[0].value))) ? parseFloat($("#max" + layer_name + "text")[0].value) : -1
+        
+        layers_filter[layer_name] = {'min': minlayer, 'max': maxlayer}
+      }
+
+      //Expression Search
+      var expressioncomparison = ''
+      var expressiondrop = $('#expressiondrop')[0].value
+      var expressionrel = $('#expressionrel')[0].value
+      var expressiontext = $('#expressiontext')[0].value
+
+      // console.log(expressiondrop, expressionrel, expressiontext)
+
+      if (expressiondrop != "Choose item" && expressionrel != "Choose operator" && expressiontext != '') {
+        if (expressionrel == '=') {
+          if (!isNaN(expressiontext)) {
+            expressioncomparison = '== ' + expressiontext
+          } else {
+            expressioncomparison = '== "' + expressiontext + '"'
+          }
+        } else if (expressionrel == '\u{2260}') {
+          if (!isNaN(expressiontext)) {
+            expressioncomparison = '!= ' + expressiontext
+          } else {
+            expressioncomparison = '!= "' + expressiontext + '"'
+          }
+        } else if (expressionrel == '\u{2264}' && !isNaN(expressiontext)) {
+          expressioncomparison = '<= ' + expressiontext
+        } else if (expressionrel == '\u{2265}' && !isNaN(expressiontext)) {
+          expressioncomparison = '>= ' + expressiontext
+        } else if (expressionrel == '\u{003C}' && !isNaN(expressiontext)) {
+          expressioncomparison = '< ' + expressiontext
+        } else if (expressionrel == '\u{003E}' && !isNaN(expressiontext)) {
+          expressioncomparison = '> ' + expressiontext
+        } else if (expressionrel == '\u{25C2}\u{25AA}\u{25B8}') {
+          expressioncomparison = '.includes("' + expressiontext + '")'
+        } else if (expressionrel == '\u{25C2}\u{25AA}') {
+          expressioncomparison = '.endsWith("' + expressiontext + '")'
+        } else if (expressionrel == '\u{25AA}\u{25B8}') {
+          expressioncomparison = '.startsWith("' + expressiontext + '")'
+        }
+      } 
+
+      // console.log(expressioncomparison)
+
+      //Function Search
+      var searchfunction = {}
+      var searchterms = $('#searchFunctionsValue')[0].value.split(",");
+      for (var source of functional_annotation_sources_available) {
+        if ($("#flex" + source).prop('checked') == true) {
+          searchfunction[source] = searchterms
+        }
+      }
+
+      console.log(searchfunction)
+
+      var layers_positions = {}
+      for (var layer_name of Object.keys(layers_filter)) {
+        
+        var minlayer = layers_filter[layer_name]['min']
+        var maxlayer = layers_filter[layer_name]['max']
+
+        if (minlayer != -1 || maxlayer != -1 || (minlayer != -1 && maxlayer != -1)) {
+
+          layers_positions[layer_name] = []
+          searchpos = true
+          if (layer_name == 'position') {
+            var global_x = data["infos"]["meta"]["global_x_offset"] -1;
+            var layerobjects = new Array(global_x - 1).fill().map((d, i) => i + 1);
+            // console.log(layerobjects)
+          } else {
+            var layerobjects = document.querySelectorAll("." + layer_name)
+          }
+
+          for (var o of layerobjects) {
+
+            var append = true
+            
+            if (layer_name == 'position') {
+              var value = o
+              var result = o
+            } else {
+              var value = o.getAttribute("name")
+              var result = o.getAttribute("xpos")
+            }
+
+            if (minlayer != '-1'){
+              if (eval(value + '<' + minlayer)){
+                append = false
+              }
+            }
+
+            if (maxlayer != '-1'){
+              if (eval(value + '>' + maxlayer)){
+                append = false
+              }
+            }
+
+            if (append == true) {
+              layers_positions[layer_name].push(parseInt(result))
+            }
+
+          }
+        }
+      }
+
+      // console.log(layers_positions)
+
+      var positions = []
+      var keys = Object.keys(layers_positions)
+
+      if (keys.length > 0) {
+        for (var pos of layers_positions[keys[0]]) {
+
+          if (keys.length > 0) {
+            var add = true
+            for (let k = 1; k < keys.length; k++) {
+              if (!layers_positions[keys[k]].includes(pos)) {
+                add = false
+              }
+            }
+
+            if (add == true) {
+              positions.push(pos)
+            }
+          } else {
+            positions.push(pos)
+          }
+        }
+      }
+        
+      // console.log(positions)
+
+      if (expressioncomparison == '' && Object.keys(searchfunction).length == 0 && searchpos == false) {
+        var message = "Please enter valid search parameters."
+      } else {
+        // console.log(expressioncomparison, searchfunction, searchpos)
+
+        var passed_gcs = await checknode(searchfunction)
+        
+        var nodes = document.querySelectorAll(".node")
+        for (var node of nodes) {
+
+          var id = node.getAttribute("id")
+          var node = data['elements']['nodes'][id]
+          
+          if (passed_gcs.includes(node['name'])) {
+            var append = true
+          } else {
+            var append = false
+          }
+
+          if (searchpos == true) {
+            if (!positions.includes(parseInt(node['position']['x_offset']))) {
+              append = false
+            }
+          }
+
+          if (append == true) {
+            if (expressiondrop == "Name") {
+              if (eval('"' + node["name"] + '"' + expressioncomparison)) {
+                if (!(id in searched)) {
+                  searched[id] = [id]
+                }
+              }
+            } else {
+              if (!(id in searched)) {
+                searched[id] = [id]
+              }
+            }
+          }
+        }
+
+        var groups = document.querySelectorAll(".group")
+        for (var group of groups) {
+          var groupid = group.getAttribute("id")
+          var members = data["infos"]["groups"][groupid]
+          for (var id of members) {
+
+            node = data['elements']['nodes'][id]
+            var append = true
+
+            if (passed_gcs.includes(node['name'])) {
+              var append = true
+            } else {
+              var append = false
+            }              
+
+            if (searchpos == true) {
+              if (!positions.includes(parseInt(node['position']['x_offset']))) {
+                append = false
+              }
+            }
+  
+            if (append == true) {
+              if (expressiondrop == "Name") {
+                if (eval('"' + node["name"] + '"' + expressioncomparison) || eval('"' + group + '"' + expressioncomparison)) {
+
+                  if (!(groupid in searched)) {
+                    searched[groupid] = [id]
+                  } else {
+                    searched[groupid].push(id)
+                  }
+                }
+              } else {
+                if (!(groupid in searched)) {
+                  searched[groupid] = [id]
+                } else {
+                  searched[groupid].push(id)
+                }
+              }
+            }
+          }
+        }
+        
+        var table = $('<div class="form-horizontal"></div>')
+
+        for (var key of Object.keys(searched)) {
+          
+          table.append(
+            $('<div class="col-12"></div>').append(
+              $('<div class="row align-items-center"></div>').append(
+                $('<div class="col-12 mb-1">' + searched[key] + '</td>')
+              )
+            )
+          )
+        }
+
+        $('#searchtable').empty()
+        $('#searchtable').append(
+          $('<div class="pt-3"></div>').append(
+            $('<div class="shadow-box pb-3 pr-3 pl-3 mb-3 rounded search-box-filter"></div>').append(
+              table
+            )
+          )
+        )
+
+        var message = 'You have ' + Object.keys(searched).length + ' item(s) in your queue.'
+
+        if (Object.keys(searched).length != 0) {
+          searchEraseButton.disabled = false;
+          searchColorButton.disabled = false;
+          searchAppendBin.disabled = false;
+          searchRemoveBin.disabled = false;
+        }
+      }
+
+      var toastbody = $('#searchtoastbody')
+      toastbody.empty()
+      toastbody.append(
+        message
+      )
+      // var searchtoast = bootstrap.Toast.getOrCreateInstance($('#searchtoast'))
+      $('#searchtoast').toast('show')
+    })
+
+    var nodes = document.querySelectorAll(".node")
+    var divs = document.querySelectorAll(".node, .group");
+    for (var el of divs) {
+
+      if (el.getAttribute("class") == 'group'){
+        var id = data["infos"]["groups"][el.getAttribute("id")][0]
+        var name = el.getAttribute("id")
+      } else {
+        var id = el.getAttribute("id")
+        var name = data['elements']['nodes'][el.getAttribute("id")]['name']
+      }
+
+      tippy(el, {
+        content: '<strong>' + name + '</strong>' + '<br />',
+        allowHTML: true,
+        onHide(instance) {
+          if (instance.reference.id.startsWith('GCG_')){
+            var id = data["infos"]["groups"][instance.reference.id][0]
+          } else {
+            var id = instance.reference.id
+          }
+          var elements = Object.keys(data['elements']['nodes'][id]['genome'])
+
+          for (var element of elements) {
+            $('#number_' + element)[0].innerText = '0';
+          }
+        },
+        onShow(instance) {
+          if (instance.reference.id.startsWith('GCG_')){
+            var id = data["infos"]["groups"][instance.reference.id][0]
+          } else {
+            var id = instance.reference.id
+          }
+          var elements = Object.keys(data['elements']['nodes'][id]['genome'])
+
+          for (var element of elements) {
+            $('#number_' + element)[0].innerText = '1';
+          }
+        },
+        arrow: false,
+        duration: 0,
+        followCursor: true,
+        theme: "light",
+      });
+    };
+
+    var isDown = false
+    var diff = 0
+
+    var old_xpos = 0
+    var old_ypos = 0
+
+    var xpos = 0
+    var ypos = 0
+
+    var new_xpos = 0
+    var new_ypos = 0
+
+    $("#svgbox").on('mousedown', function(e) {
+      old_xpos = e.offsetX
+      old_ypos = e.offsetY
+
+      xpos = old_xpos
+      ypos = old_ypos
+
+      isDown = true
+      diff = 0
+    })
+
+    $("#svgbox").on('mousemove', function(e) {
+      if (isDown === true) {
+        new_xpos = e.offsetX
+        new_ypos = e.offsetY
+
+        diff += Math.sqrt((new_xpos-xpos)^2+(new_ypos-ypos)^2)
+
+        if (!e.shiftKey) {
+          window.zoomSVG.panBy({x: new_xpos-xpos, y: new_ypos-ypos})
+        }
+
+        xpos = new_xpos
+        ypos = new_ypos
+      }
+    })
+
+    $("#svgbox").on('mouseup', function(e) {
+      if (isDown === true) {
+
+        var selection = document.querySelector('input[name="binradio"]:checked')
+
+        isDown = false
+
+        if (diff < 10) {
+          if (e.target.getAttribute('class') === 'group' || e.target.getAttribute('class') === 'node') {
+
+            if (e.shiftKey && selection !== null) {
+
+              var binid = selection.value
+              bins = marknode(e.target, data, binid, bins);
+
+            } else {
+              //show_node_details_modal(e.target, data);
+              // console.log(e.target)
+              nodeinfo(e.target, data);
+            }
+
+          } else {
+          }
+
+        } else {
+          if (e.shiftKey && selection !== null) {
+
+            var binid = selection.value
+
+            var max_xpos = Math.max(old_xpos, xpos)
+            var min_xpos = Math.min(old_xpos, xpos)
+
+            var max_ypos = Math.max(old_ypos, ypos)
+            var min_ypos = Math.min(old_ypos, ypos)
+
+            for (var n of nodes) {
+
+              var bounding = n.getBoundingClientRect();
+              var left = bounding.left
+              var right = bounding.right
+              var bottom = bounding.bottom
+              var top = bounding.top
+
+              if (
+                min_xpos < left &&
+                max_xpos > right &&
+                min_ypos < bottom &&
+                max_ypos > top
+                ) {
+                bins = marknode(n, data, binid, bins);
+
+              }
+            }
+
+            var groups = data['infos']['groups']
+            for(var g in groups) {
+              // var inside = true;
+              var group = data['infos']['groups'][g]
+              for (var k of group) {
+                var node = document.getElementById(k);
+
+                var bounding = node.getBoundingClientRect();
+                var left = bounding.left
+                var right = bounding.right
+                var bottom = bounding.bottom
+                var top = bounding.top
+
+                if (
+                  min_xpos < left &&
+                  max_xpos > right &&
+                  min_ypos < bottom &&
+                  max_ypos > top
+                  ) {
+                  var name = document.getElementById(g);
+                  bins = marknode(name, data, binid, bins);
+                  break
+                }
+                // if (
+                //   min_xpos < left &&
+                //   max_xpos > right &&
+                //   min_ypos < bottom &&
+                //   max_ypos > top
+                //   ) {
+                // } else {
+                //   inside = false
+                // }
+              }
+
+              // if (inside === true){
+              //   var name = document.getElementById(g);
+              //   bins = marknode(name, data, binid, bins);
+              // }
+            }
+          }
+        }
+      }
+    })
+    document.body.addEventListener('keydown', function(ev) {
+      if ((/^(?:input|select|textarea|button)$/i).test(ev.target.nodeName))
+      {
+          // shortcuts should not work if user is entering text to input.
+          return false;
+      }
+      if (ev.keyCode === 83) { // S = 83
+          $('#toggle-panel-left').trigger('click');
+      }
+      if (ev.keyCode === 84) { // T = 84
+          $('#title-panel').toggle();
+          $('#toggle-panel-top').toggleClass('invisible visible');
+      }
+    });
+  }})
+
+}
+
+//ANCHOR - Main function after loading DOM
+$(document).ready(function() {
+
+  // console.log('start pangrah layout creation!')
+  main()
+
+});
diff --git a/anvio/data/interactive/package.json b/anvio/data/interactive/package.json
index 55bba502f..7e33253a7 100644
--- a/anvio/data/interactive/package.json
+++ b/anvio/data/interactive/package.json
@@ -34,6 +34,7 @@
     "randomcolor": "0.6.2",
     "sortable-tablesort": "3.2.2",
     "svg-pan-zoom": "3.6.1",
+    "tippy.js": "6.3.7",
     "toastr": "2.1.2"
   }
 }
diff --git a/anvio/data/interactive/pangraph.html b/anvio/data/interactive/pangraph.html
new file mode 100644
index 000000000..58dc6c93c
--- /dev/null
+++ b/anvio/data/interactive/pangraph.html
@@ -0,0 +1,714 @@
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    
+    <title>Gene Cluster Network</title>
+
+    <link type="text/css" rel="stylesheet" href="./node_modules/bootstrap/dist/css/bootstrap.css" />
+    <link type="text/css" rel="stylesheet" href="./node_modules/bootstrap-icons/font/bootstrap-icons.min.css" />
+    <link rel="stylesheet" href="./node_modules/jquery-ui/themes/base/draggable.css">
+    <!-- <link type="text/css" rel="stylesheet" href="lib/pangraph/tippy.js/themes/light.css" />
+    <link type="text/css" rel="stylesheet" href="lib/pangraph/tippy.js/dist/tippy.css" /> -->
+    <link type="text/css" rel="stylesheet" href="css/pangraph.css" />
+    <link rel="shortcut icon" href="#">
+    <link href="./node_modules/sortable-tablesort/sortable.min.css" rel="stylesheet">
+    <script type="text/javascript" src="./node_modules/jquery/dist/jquery.min.js" onerror='alertDependencyError("jquery-core")'></script>
+    <script type="text/javascript" src="./node_modules/html5sortable/dist/html5sortable.min.js" onerror='alertDependencyError("html5sortable")'></script>
+
+    <script>$.uiBackCompat = false; //Do not change the order of jquery-ui files</script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/jquery-patch.js" onerror='alertDependencyError("jquery-patch")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widget.js" onerror='alertDependencyError("jquery-widget")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/mouse.js" onerror='alertDependencyError("jquery-mouse")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/plugin.js" onerror='alertDependencyError("jquery-plugin")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/draggable.js" onerror='alertDependencyError("jquery-draggable")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/resizable.js" onerror='alertDependencyError("jquery-core")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/sortable.js" onerror='alertDependencyError("jquery-sortable")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/widgets/button.js" onerror='alertDependencyError("jquery-button")'></script>
+    <script type="text/javascript" src="./node_modules/jquery-ui/ui/position.js" onerror='alertDependencyError("jquery-position")'></script>
+    
+    <script type="text/javascript" src="./node_modules/@popperjs/core/dist/umd/popper-lite.js" onerror='alertDependencyError("popper")'></script>
+    <script type="text/javascript" src="./node_modules/tippy.js/dist/tippy-bundle.umd.min.js" onerror='alertDependencyError("tippy-bundle")'></script>
+    <script type="text/javascript" src="./node_modules/bootstrap/dist/js/bootstrap.min.js" onerror='alertDependencyError("bootstrap")'></script>
+    <script type="text/javascript" src="./node_modules/svg-pan-zoom/dist/svg-pan-zoom.min.js" onerror='alertDependencyError("svg-pan-zoom")'></script>
+    <script type="text/javascript" src="./node_modules/sortable-tablesort/sortable.min.js" onerror='alertDependencyError("table-sorter")'></script>
+    <script type="text/javascript" src='js/pangraph.js' type="module"></script>
+    <script type="text/javascript" src="js/animations.js"></script>
+    <script type="text/javascript" src="js/context-menu.js"></script>
+    <script type="text/javascript" src="js/tree.js"></script>
+    <script type="text/javascript" src="js/utils.js"></script>
+
+  </head>
+
+  <body>
+    <div id="wrapper">
+      <div class="invisible" id="toggle-panel-top" onclick="$('#toggle-panel-top').toggleClass('visible invisible'); $('#title-panel').show();">
+          &#9660; TITLE
+      </div>
+      <div id="title-panel">
+          <div id="title-alter-panel">
+              <span id="title-panel-first-line"></span><br>
+              <span id="title-panel-second-line"></span>
+              <div id="title-panel-close-button">
+                  <a href="#" class="close-thick" onclick="$('#title-panel').hide(); $('#toggle-panel-top').toggleClass('invisible visible');"></a>
+              </div>
+          </div>
+      </div>
+      <div id="toggle-panel-left" class="toggle-panel-left-pos" onclick="toggleLeftPanel();">
+        <span id="toggle-panel-left-inner">&#9664;</span><span style="display: block; font-size: 11px; transform: rotate(90deg);"><u>S</u>ETTINGS</span>
+      </div>
+    </div>
+
+    <div id="svgbox"></div>
+
+    <div id="panel-left">
+      <div class="d-flex" id="sidebar" onload="{$('#support_value_params').hide()}">
+          <div class="inner-wrapper d-flex" role="tabpanel">
+              <nav id="inner-sidebar" onclick="switchNavigationTabs();">
+                  <ul class="list-unstyled components align-item-center text-center tab-elements" role="tablist" id="nav-tab">
+                      <li id="main_tab" role="presentation" class="nav-item navigation-tabs mt-1">
+                          <a href="#main_settings" aria-controls="main_settings" role="tab" data-toggle="tab" class="nav-link navbar-btn d-block active">
+                              <i class="nav-icon fs-2x bi bi-house-door"></i><i class="nav-icon-fill fs-2x bi bi-house-door-fill"></i> <span class="d-block">Main</span>
+                          </a>
+                      </li>
+                      <li id="bin_settings_tab" role="presentation" class="nav-item">
+                          <a href="#bin_settings" aria-controls="bin_settings" role="tab" data-toggle="tab" class="nav-link navbar-btn d-block">
+                              <i class="nav-icon fs-2x bi bi-archive "></i><i class="nav-icon-fill fs-2x bi bi-archive-fill "></i><span class="d-block">Bins</span>
+                          </a>
+                      </li>
+                      <li id="data_panel_tab" role="presentation" class="nav-item">
+                          <a href="#data_tab"  aria-controls="data_tab" role="tab" data-toggle="tab"  class="nav-link navbar-btn d-block" >
+                              <i class="nav-icon fs-2x bi bi-cursor"></i><i class="nav-icon-fill fs-2x bi bi-cursor-fill"></i><span role="tab" class="d-block">Data</span>
+                          </a>
+                      </li>
+                      <li id="search_panel_tab" role="presentation" class="nav-item">
+                          <a href="#search_tab" aria-controls="search_tab" role="tab" data-toggle="tab" class="nav-link navbar-btn d-block">
+                              <i class="nav-icon fs-2x bi bi-search"></i><i class="nav-icon-fill fs-2x bi bi-search"></i><span class="d-block">Search</span>
+                          </a>
+                      </li>
+                      <li id="detail_tab" role="presentation" class="nav-item">
+                          <a href="#anvio_detail_tab" aria-controls="anvio_detail_tab" role="tab" data-toggle="tab" class="nav-link navbar-btn d-block">
+                              <i class="nav-icon fs-2x bi bi-question-octagon"></i><i class="nav-icon-fill fs-2x bi bi-question-octagon-fill"></i><span class="d-block">Anvi'o</span>
+                          </a>
+                      </li>
+                      <div id="nav-bottom">
+                          <li class="nav-bottom-alignment">
+                              <a href="" class="navbar-btn d-block glow-on-hover" id="redraw" data-help="draw-button" onclick="return false;">
+                                  <i class="icon-unlock bi-pencil fs-2x"></i><span class="d-block"><u>D</u>raw</span>
+                              </a>
+                          </li>
+                          <hr class="nav-bottom-alignment border-color">
+                          <li class="nav-bottom-alignment">
+                              <p class="side-menu-text">State</p>
+                              <li class="nav-bottom-alignment disabled">
+                                  <a href="#" class="navbar-btn d-block mt-3" onclick="showLoadStateWindow();" data-help="load-state-button">
+                                      <i class="icon-unlock bi bi-upload fs-2x"></i><span class="d-block">Load</span>
+                                  </a>
+                              </li>
+                              <li class="nav-bottom-alignment disabled"><a href="#" class="navbar-btn d-block" onclick="showSaveStateWindow();" data-help="save-state-button" disabled-in-read-only="true"><i class="icon-unlock bi bi-download fs-2x"></i><span class="d-block">Save</span> </a></li>
+                          </li>
+                          <hr class="nav-bottom-alignment border-color">
+                          <p class="side-menu-text nav-bottom-alignment">Display</p> 
+                          <li class="nav-bottom-alignment">
+                              <a href="#" class="navbar-btn d-block" id="svgDownload" data-help="save-svg">
+                                  <i class="icon-unlock bi bi-images fs-2x"></i><span class="d-block">Export</span>
+                              </a>
+                          </li>
+                          <li class="nav-bottom-alignment pb-2">
+                              <a id="fit" href="#" class="navbar-btn d-block justify-content-center" data-help="return-to-natural">
+                                  <i class="icon-unlock bi bi-align-middle fs-2x"></i><span class="d-block">Align</span>
+                              </a>
+                          </li>
+                      </div>
+                  </ul>
+              </nav>
+          </div>
+
+          <div class="col-11 tab-content ml-1">
+            <!-- MAIN Tab -->
+            <div role="tabpanel" class="tab-pane fade show active" id="main_settings">
+                <div id="tree-settings" class="form-horizontal">
+                  <span id="toggle-chevron-item" class="settings-header btn d-flex chart-icon-padding align-items-center" data-toggle="collapse" href="#item-collapse-main" role="button" aria-expanded="true" aria-controls="item-collapse-option" onclick="$('#toggle-chevron-item').children('i').toggleClass('bi-chevron-up bi-chevron-down');">
+                    <img src="images/item-chart.svg" alt="Item Icon"/> 
+                    Items
+                    <i class="text-secondary ml-1 d-flex pt-1 align-items-center bi bi-chevron-down"></i>
+                  </span> 
+
+                  <div id="item-collapse-main" class="ml-2 mr-3 collapse multi-collapse show">
+                    <span class="settings-secondary-header mb-3 mt-3">Color</span>
+
+                    <div class="row align-items-center">
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Color groups
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="color" class="form-control form-control-color flex-fill p-0 border-0" id=groups name=groups value="#800080" aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Color nodes 
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="color" class="form-control form-control-color flex-fill p-0 border-0" id=nodes name=nodes value="#bcbcbc" aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Color layers 
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="color" class="form-control form-control-color flex-fill p-0 border-0" id=layer_color name=layer_color value="#f5f5f5" aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+
+                      <div class="col-12 d-flex mb-1 py-1">      
+                        <div class="col-2 d-flex align-items-center">
+                          <input type="checkbox" id="flexsaturation" name="flexsaturation" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top" checked>
+                        </div>
+                        <div class="col-10 d-flex align-items-center">
+                          Saturation by significance
+                        </div>
+                      </div>                
+                    </div>
+
+                    <span class="settings-secondary-header mb-3 mt-3">Layers</span>
+
+                    <div id="layers" class="row align-items-center">
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                          <div class="form-switch d-flex">
+                            <input class="" type="checkbox" id="flexarrow" name="flexarrow" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top" checked>
+                          </div>
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Orientation arrow
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="arrow" name="arrow" value=100 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                    </div>
+                    
+                    <span class="settings-secondary-header mb-3 mt-3">Phylogenie</span>
+                    
+                    <div class="row align-items-center">
+
+                      <div class="col-12 d-flex mb-1 py-1">      
+                        <div class="col-2 d-flex align-items-center">
+                          <input type="checkbox" id="flextree" name="flextree" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">
+                        </div>
+                        <div class="col-10 d-flex align-items-center">
+                          Show phylogenic tree
+                        </div>
+                      </div>      
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Tree length
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="tree" name="tree" value=500 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Tree offset
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="tree_offset" name="tree_offset" value=100 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Tree line thickness
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="tree_thickness" name="tree_thickness" value=3 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                    </div>
+
+                    <span class="settings-secondary-header mb-3 mt-3">Nodes & Edges</span>
+
+                    <div class="row align-items-center mb-3">
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Node x-distance
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="distx" name="distx" value=30 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Node y-distance
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="disty" name="disty" value=30 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Node radius
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="size" name="size" value=10 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Node line thickness
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="circ" name="circ" value=2 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Edge thickness
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="edge" name="edge" value=2 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                    </div>
+                      
+                    <span class="settings-secondary-header mb-3 mt-3">Others</span>
+
+                    <div class="row align-items-center mb-3">
+                      <div class="col-12 d-flex mb-1 py-1">      
+                        <div class="col-2 d-flex align-items-center">
+                          <input type="checkbox" id="flexlinear" name="flexlinear" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">
+                        </div>
+                        <div class="col-10 d-flex align-items-center">
+                          Linear graph layout
+                        </div>
+                      </div>      
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Line graph thickness
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="line" name="line" value=1 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Label size
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="label" name="label" value=12 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Search hit size
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="search_hit" name="search_hit" value=200 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Inner layer margin
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="inner_margin" name="inner_margin" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Outer layer margin
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="outer_margin" name="outer_margin" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Additional inner radius
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="inner" name="inner" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                    </div>
+
+                    <span class="settings-secondary-header mb-3 mt-3">Graph</span>
+                    <div class="row align-items-center">
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                          <div class="form-switch d-flex">
+                            <input class="" type="checkbox" id="flexcondtr" name="flexcondtr" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top" checked>
+                          </div>
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Merge nodes into groups
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="condtr" name="condtr" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                          <div class="form-switch d-flex">
+                            <input class="" type="checkbox" id="flexmaxlength" name="flexmaxlength" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top" checked>
+                          </div>
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Allowed max edge length
+                        </div>
+                        <div class="d-flex col-2">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="maxlength" name="maxlength" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color" disabled>
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                          <div class="form-switch d-flex">
+                            <input class="" type="checkbox" id="flexgroupcompress" name="flexgroupcompress" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top" checked>
+                          </div>
+                        </div>
+                        <div class="col-8 d-flex align-items-center">
+                          Group size compression
+                        </div>
+                        <div class="col-2 d-flex">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="groupcompress" name="groupcompress" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                        </div>
+                      </div>
+                      <div class="col-12 d-flex mb-1">
+                        <div class="col-2 d-flex align-items-center">
+                          <div class="form-switch d-flex">
+                            <input class="" type="checkbox" id="flexungroup" name="flexungroup" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top">
+                          </div>
+                        </div>
+                        <div class="col-6 d-flex align-items-center">
+                          Ungroup area
+                        </div>
+                        <div class="col-2 d-flex">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="ungroupfrom" name="ungroupfrom" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color" disabled>
+                        </div>
+                        <div class="col-2 d-flex">
+                          <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="ungroupto" name="ungroupto" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color" disabled>
+                        </div>
+                      </div>
+                    </div>
+
+                    <span class="settings-secondary-header mb-3 mt-3">Genomes</span>
+                    
+                    <div id="genomecolors" class="row grid align-items-center sortable">
+                    </div>
+                  </div>
+                </div>
+              </div>
+
+            <!-- BIN Tab -->
+            <div role="tabpanel" class="tab-pane fade show" id="bin_settings">
+              <div id="bin-settings" class="form-horizontal mt-3">  
+                <div class="panel-body">
+                  <span class="settings-secondary-header mb-3 mt-3">Bins</span>
+                  
+                  <div class="row align-items-center ml-2 mr-3">
+                    <div class="col-12">
+    
+                      <div class="row grid align-items-center" id="bingrid">
+                        <div class="col-12" id="bin1">
+                          <div class="row align-items-center">
+                            <div class="col-2">
+                              <input type="radio" name="binradio" id="bin1radio" value="bin1" aria-label="..." data-toggle="tooltip" data-placement="top" title="Tooltip on top" checked>
+                            </div>
+                            <div class="col-6">
+                              <input type="text" class="form-control flex-fill p-0 border-0" style= "background-color: #e9ecef;" value="Bin_1" id="bin1text" aria-describedby="">
+                            </div>
+                            <div class="d-flex col-2">
+                              <input type="text" class="form-control float-end text-end flex-fill p-0 border-0" style= "background-color: #e9ecef;" id="bin1value" value=0 aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color" readonly>
+                            </div>
+                            <div class="d-flex col-2">
+                              <input type="color" class="form-control form-control-color flex-fill p-0 border-0 colorchange" id=bin1color name="bin1" value="#000000" aria-label="..." data-toggle="tooltip" data-placement="top" title="Choose your color">
+                            </div>
+                          </div>
+                        </div>
+                      </div>
+                    </div>
+                  </div>
+                  <div class="pt-5">
+                    <div class="col-12 pt-2 border-top d-flex align-items-center justify-content-center">
+                      <button type="button" class="col-6 btn btn-outline-success btn-md mr-2 align-items-center justify-content-center" id="binadd">
+                        <i class="bi bi-archive-fill fa-lg bin-icon-size" aria-hidden="true"></i>
+                        <span class="font-weight-bold">Add bin</span>
+                      </button>
+                      <button type="button" class="col-6 btn btn-outline-danger btn-md align-items-center justify-content-center" id="binremove">
+                        <i class="bi bi-trash3-fill fa-lg bin-icon-size" aria-hidden="true"></i>
+                        <span class="font-weight-bold">Delete bin</span>
+                      </button>
+                    </div>
+                    <div class="col-12 pt-2 d-flex align-items-center justify-content-center">
+                      <button type="button" class="col-3 btn btn-outline-secondary btn-md mr-1 align-items-center justify-content-center" id="binload" disabled>
+                        <i class="bi bi-arrow-up-square fa-lg bin-icon-size" aria-hidden="true"></i>
+                        <span class="font-weight-normal">Load bins</span>
+                      </button>
+                      <button type="button" class="col-3 btn btn-outline-secondary btn-md mr-1 align-items-center justify-content-center" id="binsave" disabled>
+                        <i class="bi bi-arrow-down-square fa-lg bin-icon-size" aria-hidden="true"></i>
+                        <span class="font-weight-normal">Store bins</span>
+                      </button>
+                      <button type="button" class="col-3 btn btn-outline-secondary btn-md align-items-center justify-content-center" id="bininfo">
+                        <i class="bi bi-info-square fa-lg bin-icon-size" aria-hidden="true"></i>
+                        <span class="font-weight-normal">Bin info</span>
+                      </button>
+                      <button type="button" class="col-3 btn btn-outline-secondary btn-md align-items-center justify-content-center" id="binanalyse">
+                        <i class="bi bi-info-square fa-lg bin-icon-size" aria-hidden="true"></i>
+                        <span class="font-weight-normal">Analyze bins</span>
+                      </button>
+                    </div>
+                  </div>
+                </div>
+              </div>
+            </div>
+
+            <!-- DATA TAB -->
+            <div role="tabpanel" class="tab-pane fade show" id="data_tab">
+              <p class="mt-3" style="color: #AAAAAA; padding: 5px;">This panel will show you information for splits when you hover them with your mouse pointer on the pangraph.</p>
+              <div id="mouse_hover">
+                <div class="offcanvas-body p-0" id="rightoffcanvas-body">
+                    <div id="right" class="ml-2" style="height: 100%; overflow: hidden;">
+                      <div class="table-responsive" style="width: 100%; position: relative;">
+                        <table class="table table-striped table-bordered sortable">
+                          <thead>
+                            <tr>
+                              <th>Genome Name</th>
+                              <th>Occurrence</th>
+                            </tr>
+                          </thead>
+                          <tbody id="RightOffcanvasBodyTop" class="sortable">
+                              <!-- JS FILLS HERE -->
+                          </tbody>
+                        </table>
+                      </div>
+                      </div>
+                  </div>
+                </div>
+
+            </div>
+
+            <!-- SEARCH Tab -->
+            <div role="tabpanel" class="tab-pane fade show" id="search_tab">
+              <div class="mt-1 p-2" id="search_tab_content" tabindex="-1">
+                <div class="shadow-box focus-box pb-3 pr-3 pl-3 mb-3 rounded search-box-expression">
+                  <span class="settings-header mb-3 pt-2" data-help='search-expression'>Search with expression</span>
+                  <div class="form-horizontal">
+                    <table class="col-12">
+                      <tr>
+                          <td class="col-3">Item:</td>
+                          <td class="col-9">
+                            <select class="form-control form-control-sm col-12 select-sm" id="expressiondrop" data-help="search-layer" disabled>
+                            </select>
+                          </td>
+                      </tr>
+                      <tr>
+                          <td class="col-3">Operator:</td>
+                          <td class="col-9">
+                              <select class="form-control form-control-sm col-12 select-sm" id="expressionrel" data-help="search-operator" disabled>
+                                  <option value="Choose operator">Choose operator</option>  
+                                  <option value="=">Equal</option>
+                                  <option class="font-weight-bold" value="&ne;">Unequal</option>
+                                  <option class="font-weight-bold" value="&le;">Less than or equal</option>
+                                  <option class="font-weight-bold" value="&ge;">Greater than or equal</option>
+                                  <option class="font-weight-bold" value="&lt;">Less than</option>
+                                  <option class="font-weight-bold" value="&gt;">Greater than</option>
+                                  <option class="font-weight-bold" value="&#9666;&#9642;&#9656;">Contains</option>
+                                  <option class="font-weight-bold" value="&#9666;&#9642;">Ends with</option>
+                                  <option class="font-weight-bold" value="&#9642;&#9656;">Starts with</option>
+                              </select>
+                          </td>
+                      </tr>
+                      <tr>
+                          <td class="col-3">Term:</td>
+                          <td class="col-9">
+                            <input class="input-search form-control form-control-sm col-12" id="expressiontext" type="text" value="" data-help="search-value" placeholder="Term" disabled>
+                          </td>
+                      </tr>
+                  </table>
+                  </div>
+                </div>
+
+                <div class="shadow-box pb-3 pr-3 pl-3 mb-3 rounded search-box-function">
+                  <span class="settings-header mb-3 pt-2">Search functions</span>
+                  <div class="form-horizontal">
+                    <div id="searchSources" class="row align-items-center">
+                    </div>
+                  
+                    <table class="col-12">
+                        <tr>
+                            <td class="col-3">Terms:</td>
+                            <td class="col-9">
+                                <input id="searchFunctionsValue" class="input-search form-control" value="" data-help="search-value" placeholder="You can separate multiple search terms with ','">
+                            </td>
+                        </tr>
+                    </table>
+                  </div>
+                </div>
+
+                <div class="shadow-box pb-3 pr-3 pl-3 mb-3 rounded search-box-filter">
+                  <span class="settings-header mb-3 pt-2">Filter</span>
+                  <div class="form-horizontal">
+                    <div id="filter" class="row align-items-center">
+                    </div>
+                  </div>
+                </div>
+
+                <div class="pt-3">
+                  <div class="col-12 pt-2 border-top d-flex align-items-center justify-content-center">
+                    <button type="button" class="col-4 btn btn-outline-primary btn-md mr-1 align-items-center justify-content-center" id="search">
+                      <i class="bi bi-search fa-lg bin-icon-size" aria-hidden="true"></i>
+                      <span class="font-weight-bold">Search</span>
+                    </button>
+                    <button type="button" class="col-4 btn btn-outline-secondary btn-md mr-1 align-items-center justify-content-center" id="searchcolor" disabled>
+                      <i class="bi bi-highlighter fa-lg" aria-hidden="true"></i>
+                      <span class="font-weight-bold">Highlight</span>
+                    </button>
+                    <button type="button" class="col-4 btn btn-outline-secondary btn-md align-items-center justify-content-center" id="searcherase" disabled>
+                      <i class="bi bi-eraser fa-lg" aria-hidden="true"></i>
+                      <span class="font-weight-bold">Remove</span>
+                    </button>
+                  </div>
+                  <div class="col-12 pt-2 d-flex align-items-center justify-content-center">
+                    <button type="button" class="col-6 btn btn-outline-success btn-md mr-2 align-items-center justify-content-center" id="searchadd" disabled>
+                      <span class="font-weight-normal">Append splits to bin</span>
+                    </button>
+                    <button type="button" class="col-6 btn btn-outline-danger btn-md align-items-center justify-content-center" id="searchremove" disabled>
+                      <span class="font-weight-normal">Remove splits from bin</span>
+                    </button>
+                  </div>
+                </div>
+
+                <div id="searchtable"></div>
+              </div>
+            </div>
+
+            <!-- ANVIO TAB -->
+            <div role="tabpanel" class="tab-pane fade show" id="anvio_detail_tab">
+              <div class="mt-3 paragraph" id="anvio_tab_content">
+                  <a href="https://anvio.org/people/">
+                      <p class="subheading">Anvi'o Authors</p>
+                  </a>
+                  <hr class="mb-3 col-11 border-color">
+                  <a href="https://anvio.org/"><p class="subheading">Anvi'o Project Page</p></a>
+                  <hr class="mb-3 col-11 border-color">
+                  <a href="https://github.com/merenlab/anvio/issues"><p class="subheading">Browse/Report Issue</p></a>
+                  <hr class="mb-3 col-11 border-color">
+                  <a href="https://anvio.org/cite/"><p class="subheading">How To Cite</p></a>
+                  <hr class="mb-3 col-11 border-color">
+              </div>
+              <div class="paragraph d-flex align-item-center justify-content-center col-10">
+                  <a href="https://discord.gg/C6He6mSNY4" class="mr-3 discord-btn btn btn-outline-secondary align-item-center justify-content-center"><i class="bi bi-discord fs-2"></i> <span class="lead">| Get Help</span></a>
+                  <a href="https://github.com/merenlab/anvio" class="btn github-btn btn-outline-secondary align-item-center justify-content-center"><i class="bi bi-github fs-2"></i> <span class="lead">| Access Code</span></a>
+              </div>
+            </div>
+
+          </div>
+        </div>
+      </div>
+
+    <div class="modal fade" id="InfoModal" aria-hidden="true" aria-labelledby="exampleModalToggleLabel" tabindex="-1">
+      <div class="modal-dialog modal-dialog-centered modal-xl">
+        <div class="modal-content">
+          <div class="modal-body overflow-auto" id="InfoModalBody">
+          </div>
+          <div class="modal-footer d-flex justify-content-center" id="InfoModalFooter">
+            <div class="d-flex btn-group">
+              <button class="btn btn-outline-success" id="InfoDownload">
+                <i class="bi bi-download"> Export Info</i>
+              </button>
+              <button class="btn btn-outline-success" id="AlignmentDownload">
+                <i class="bi bi-download"> Export Alignment</i>
+              </button>
+              <button class="btn btn-outline-success" id="AddBin">
+                <i class="bi bi-archive-fill"> Bin Add/Remove </i>
+              </button>
+            </div>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <div class="modal fade" id="BinModal" aria-hidden="true" aria-labelledby="exampleModalToggleLabel" tabindex="-1">
+      <div class="modal-dialog modal-dialog-centered modal-xl">
+        <div class="modal-content">
+          <!-- <div class="modal-header">
+            <h5 class="modal-title border-bottom-0" id="BinModalTitle">Bin Information</h5>
+            <button type="button" class="close d-flex" data-dismiss="modal" aria-label="Close" aria-hidden="true">
+              <i class="bi bi-x-lg"></i>
+            </button>
+          </div> -->
+          <div class="modal-body overflow-auto" id="BinModalBody">
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <div class="modal fade" id="BinAnalyse" aria-hidden="true" aria-labelledby="exampleModalToggleLabel" tabindex="-1">
+      <div class="modal-dialog modal-dialog-centered modal-xl">
+        <div class="modal-content">
+          <!-- <div class="modal-header">
+            <h5 class="modal-title border-bottom-0" id="BinModalTitle">Bin Information</h5>
+            <button type="button" class="close d-flex" data-dismiss="modal" aria-label="Close" aria-hidden="true">
+              <i class="bi bi-x-lg"></i>
+            </button>
+          </div> -->
+          <div class="modal-body overflow-auto" id="BinAnalyseBody">
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <div class="position-fixed bottom-0 right-0 p-3" style="z-index: 5; right: 0; bottom: 0;">
+      <div id="searchtoast" class="toast hide" role="alert" aria-live="assertive" aria-atomic="true" data-delay="2000">
+        <div class="toast-header">
+          <strong class="mr-auto">Your search</strong>
+          <button type="button" class="ml-2 mb-1 close" data-dismiss="toast" aria-label="Close">
+            <span aria-hidden="true">&times;</span>
+          </button>
+        </div>
+        <div class="toast-body" id="searchtoastbody">
+        </div>
+      </div>
+    </div>
+    
+
+  </body>
+</html>
diff --git a/anvio/docs/__init__.py b/anvio/docs/__init__.py
index 14d26e78a..09e9e037f 100644
--- a/anvio/docs/__init__.py
+++ b/anvio/docs/__init__.py
@@ -621,6 +621,18 @@
         "provided_by_anvio": True,
         "provided_by_user": False
     },
+    "pan-graph-json": {
+        "name": "PAN GRAPH JSON",
+        "type": "JSON",
+        "provided_by_anvio": True,
+        "provided_by_user": False
+    },
+    "pan-graph": {
+        "name": "PAN GRAPH",
+        "type": "CONCEPT",
+        "provided_by_anvio": True,
+        "provided_by_user": False
+    },
     "interactive": {
         "name": "INTERACTIVE DISPLAY",
         "type": "DISPLAY",
diff --git a/anvio/filesnpaths.py b/anvio/filesnpaths.py
index 2ac5ea540..f7d429bd7 100644
--- a/anvio/filesnpaths.py
+++ b/anvio/filesnpaths.py
@@ -269,14 +269,18 @@ def is_file_json_formatted(file_path):
     return True
 
 
-def is_file_fasta_formatted(file_path):
+def is_file_fasta_formatted(file_path, dont_raise=False):
     is_file_exists(file_path)
 
     try:
         f = u.SequenceSource(file_path)
     except u.FastaLibError as e:
-        raise FilesNPathsError("Someone is not happy with your FASTA file '%s' (this is "
-                           "what the lib says: '%s'." % (file_path, e))
+        if dont_raise:
+            f.close()
+            return False
+        else:
+            raise FilesNPathsError("Someone is not happy with your FASTA file '%s' (this is "
+                               "what the lib says: '%s'." % (file_path, e))
 
     f.close()
 
diff --git a/anvio/interactive.py b/anvio/interactive.py
index 07e9c3cb2..13afed649 100644
--- a/anvio/interactive.py
+++ b/anvio/interactive.py
@@ -5,6 +5,7 @@
 import os
 import sys
 import copy
+import json
 import numpy
 import argparse
 import textwrap
@@ -2979,6 +2980,80 @@ def get_metabolism_data(self):
         return self.estimator.get_metabolism_data_for_visualization()
 
 
+class PangraphInteractive(PanSuperclass):
+    def __init__(self, args, run=run, progress=progress):
+        self.mode = "pangraph"
+
+        self.args = args
+        self.run = run
+        self.progress = progress
+
+        A = lambda x: self.args.__dict__[x] if x in self.args.__dict__ else None
+        self.pan_graph_json_path = A('pan_graph_json')
+        self.pan_graph_summary_path = A('pan_graph_summary')
+
+        if self.pan_graph_json_path:
+            filesnpaths.is_file_json_formatted(self.pan_graph_json_path)
+
+        if self.pan_graph_summary_path:
+            filesnpaths.is_file_json_formatted(self.pan_graph_summary_path)
+
+        if not self.pan_graph_json_path:
+            raise ConfigError("Unfortunately you can only use this program with the `--pan-graph-json` parameter.")
+
+        if A('pan_db'):
+            PanSuperclass.__init__(self, self.args)
+        else:
+            self.run.warning("Since you did not provide anvi'o with a pan-db file, this program will initiate "
+                             "the pangenome graph interface with the JSON file you have provided",
+                             header="NO PAN DB, BUT ALL GOOD 👍", lc="yellow")
+
+        self.pan_graph_json = self.get_pangraph_json()
+        self.pan_graph_summary = self.get_pangraph_summary()
+
+
+    def get_pangraph_json(self):
+        """A function to 'get' pangraph JSON data from wherever appropriate.
+
+        Currently this function returns the user-provided JSON data, but it
+        will take into consideration other parameters and pan-db to determine
+        which resource is the most appropriate to retrieve the pangraph data.
+        """
+
+        if self.pan_graph_json_path:
+            json_data = json.load(open(self.pan_graph_json_path))
+        else:
+            # FIXME: this is where we will get things from the pan-db, but it
+            #        is not yet implemented
+            raise ConfigError("Not implemented.")
+
+        # make sure the JSON data we have access is compatible with the codebase
+        # we are running.
+        version_we_have = str(json_data['infos']['meta']['version']) if 'version' in json_data['infos']['meta'] else None
+        version_we_want = str(t.pangraph_json_version)
+
+        if version_we_have == None:
+            raise ConfigError("Bad news: the pan-graph data you have is outdated :/ You will have to re-run "
+                              "the program `anvi-pan-graph` on these data to generate an up-to-date "
+                              "pan-graph artifact that your current codebase can work with.")
+
+        if version_we_have != version_we_want:
+            raise ConfigError(f"We have a problem here. The data for your pan-graph is at version {version_we_have}. "
+                              f"Yet the anvi'o codebase you have here can only work with pan-graph version {version_we_want}. "
+                              f"The best solution to address this mismatch is to re-run the program `anvi-pan-graph` "
+                              f"on your dataset.")
+
+        # all good with the version stuff:
+        return json_data
+
+
+    def get_pangraph_summary(self):
+        if self.pan_graph_summary_path:
+            summary_data = json.load(open(self.pan_graph_summary_path))
+
+            return summary_data
+
+
 class ContigsInteractive():
     def __init__(self, args, run=run, progress=progress):
         self.mode = 'contigs'
diff --git a/anvio/panops.py b/anvio/panops.py
index 3126dcb7b..2db8069c5 100644
--- a/anvio/panops.py
+++ b/anvio/panops.py
@@ -10,7 +10,17 @@
 import json
 import math
 import copy
+import argparse
 import pandas as pd
+import networkx as nx
+import numpy as np
+import itertools as it
+import matplotlib.pyplot as plt
+# from scipy.stats import entropy
+from scipy.cluster.hierarchy import linkage, fcluster, dendrogram, to_tree
+from scipy.spatial.distance import cdist, squareform
+import random
+
 from itertools import chain
 
 # multiprocess is a fork of multiprocessing that uses the dill serializer instead of pickle
@@ -30,6 +40,7 @@
 import anvio.filesnpaths as filesnpaths
 import anvio.tables.miscdata as miscdata
 
+from anvio.dbinfo import DBInfo
 from anvio.drivers.blast import BLAST
 from anvio.drivers.diamond import Diamond
 from anvio.drivers.mcl import MCL
@@ -56,6 +67,7 @@
 additional_param_sets_for_sequence_search = {'diamond'   : '--masking 0',
                                              'ncbi_blast': ''}
 
+
 class Pangenome(object):
     def __init__(self, args=None, run=run, progress=progress):
         self.args = args
@@ -1091,3 +1103,2179 @@ def process(self):
 
 
         self.run.quit()
+
+
+class Pangraph():
+    def __init__(self, args, run=run, progress=progress):
+        self.args = args
+        self.run = run
+        self.progress = progress
+
+        A = lambda x: args.__dict__[x] if x in args.__dict__ else None
+        # important Anvi'o artifacts that are necessary for successfull execution
+        self.pan_db = A('pan_db')
+        self.external_genomes_txt = A('external_genomes')
+        self.genomes_storage_db = A('genomes_storage')
+
+        # additional optinal input variables
+        self.testing_yaml = A('testing_yaml')
+        self.pan_graph_json = A('pan_graph_json')
+        self.gene_additional_data = A('gene_additional_data')
+        self.gc_additional_data = A('gc_additional_data')
+
+        # additional variables for presetting the UI values
+        self.max_edge_length_filter = A('max_edge_length_filter')
+        self.gene_cluster_grouping_threshold = A('gene_cluster_grouping_threshold')
+        self.groupcompress = A('gene_cluster_grouping_compression')
+        self.ungroup = A('ungrouping_area')
+        self.pass_filter = 0
+
+        # additional variables for special cases e.g. a user wants to tune the tool
+        # in a very specific direction
+        # TODO: skip genomes might be a very useful function
+        self.priority_genome = A('priority_genome')
+        
+        if A('genome_names'):
+            self.genomes_names = A('genome_names').split(',')
+        else:
+            self.genomes_names = []
+
+        if A('genome_reverse'):
+            self.genomes_reverse = A('genome_reverse').split(',')
+        else:
+            self.genomes_reverse = []
+
+        # the different data storage related variables e.g. input and output files
+        # TODO: DB storage is not yet implemented -> will be GRAPH.db at one point
+        self.skip_storing_in_pan_db = True
+        self.json_output_file_path = A('output_pan_graph_json')
+
+        self.output_graphml = A('output_graphml')
+        self.output_yaml = A('output_testing_yaml')
+        self.output_summary = A('output_dir_summary')
+        self.output_graphics = A('output_dir_graphics')
+
+        self.output_raw_gc_additional_data = A('output_raw_gc_additional_data')
+        self.output_raw_gene_additional_data = A('output_raw_gene_additional_data')
+
+        # learn what gene annotation sources are present across all genomes if we
+        # are running things in normal mode
+        if not self.testing_yaml and not self.pan_graph_json:
+            self.functional_annotation_sources_available = DBInfo(self.genomes_storage_db, expecting='genomestorage').get_functional_annotation_sources()
+        else:
+            self.functional_annotation_sources_available = []
+
+        # dictionary containing the layer information that will be saved in the
+        # json file to be used in the front end
+        self.data_table_dict = {}
+
+        # this is the dictionary that wil keep all data that is going to be loaded
+        # from anvi'o artifacts
+        self.gene_synteny_data_dict = {}
+        self.genomes = []
+
+        # these are the main graph data structures for the different steps of the tools execution
+        self.initial_graph = nx.DiGraph()
+        self.pangenome_graph = nx.DiGraph()
+        self.edmonds_graph = nx.DiGraph()
+        self.ancest = nx.DiGraph()
+
+        # additional self variables that are used during the tools execution
+        self.single_copy_core = set()
+        self.grouping = {}
+        self.project_name = ''
+        self.global_y = 0
+        self.global_x = 1
+        self.global_x_offset = 0
+        self.k = 0
+        self.genome_gc_occurence = {}
+        self.ghost = 0
+        self.debug = False
+        self.jsondata = {}
+        self.position = {}
+        self.offset = {}
+        self.x_list = {}
+        self.path = {}
+        self.edges = {}
+        self.layers = []
+        self.removed = set()
+
+    def sanity_check(self):
+
+        """Sanity check for incompatible settings, like skip storing and no output path"""
+
+        if self.skip_storing_in_pan_db and not self.json_output_file_path:
+            raise ConfigError("You are initializing the Pangraph class with `--skip-storing-in-pan-db` without an `--output-pan-graph-json` "
+                            "parameter for the graph results to be stored. Please set an output file path so anvi'o has at least one "
+                            "way to store results.")
+    
+        # if not self.genomes_names:
+        #     raise ConfigError("Please be nice enough to use a genome name that is present in your dataset, you know, to let the code take the wheel.")
+
+
+    def process(self):
+        """Primary driver function for the class"""
+
+        self.sanity_check()
+
+        # the pathway over the pan_graph_json serves the purpose of updating the
+        # json file
+        if self.pan_graph_json:
+            self.load_graph_from_json_file()
+
+        if not self.pan_graph_json and self.testing_yaml:
+            # skip sanity check EVERYTHING in case of testing mode
+            self.prepare_yaml()
+
+        if not self.pan_graph_json and not self.testing_yaml:
+            # populate self.gene_synteny_data_dict
+            self.get_gene_synteny_data_dict()
+
+        if not self.pan_graph_json and self.output_yaml:
+            self.export_gene_synteny_to_yaml()
+
+        if not self.pan_graph_json and not self.output_yaml:
+            # contextualize paralogs
+            # TODO Incorporate gene direction
+            self.run_contextualize_paralogs_algorithm()
+
+            # build graph
+            self.build_graph()
+
+            # reconnect open leaves in the graph to generate
+            # a flow network from left to right
+            self.run_tree_to_flow_network_algorithm()
+
+            self.prepare_synteny_graph()
+
+        if not self.output_yaml:
+            self.run_synteny_layout_algorithm()
+
+        if not self.pan_graph_json and not self.output_yaml and not self.testing_yaml:
+            # run Alex's layout algorithm
+            self.generate_data_table()
+
+        if not self.output_yaml and self.output_raw_gc_additional_data:
+            self.get_additional_gc_layer_table()
+
+        if not self.output_yaml and self.output_raw_gene_additional_data:
+            self.get_additional_gene_layer_table()
+
+        if not self.pan_graph_json and not self.output_yaml and self.gc_additional_data:
+            self.add_additional_gc_layer_values()
+
+        if not self.pan_graph_json and not self.output_yaml and self.gene_additional_data:
+            self.add_additional_gene_layer_values()
+
+        if not self.pan_graph_json and not self.output_yaml and self.output_summary:
+            self.get_genomic_motifs()
+
+        if not self.pan_graph_json and not self.output_yaml:
+            self.get_json_dict_for_graph()
+
+        if self.pan_graph_json:
+            self.update_json_dict()
+
+        if not self.output_yaml:
+            # store network in the database
+            self.store_network()
+
+
+    def prepare_yaml(self):
+        yaml_genomes = utils.get_yaml_as_dict(self.testing_yaml)
+        self.project_name = 'YAML TEST'
+
+        for genome in yaml_genomes.keys():
+            self.gene_synteny_data_dict[genome] = {}
+
+            if genome in self.genomes_names:
+                self.genomes.append(genome)
+                self.run.info_single(f"Loaded genome {genome}.")
+            else:
+                self.run.info_single(f"Skipped genome {genome}.")
+
+            for i, gcs in enumerate(yaml_genomes[genome]):
+
+                contig = genome + '_' + str(i).zfill(5)
+
+                self.gene_synteny_data_dict[genome][contig] = {}
+
+                for j, gc in enumerate(gcs.split(' ')):
+                    if gc.endswith('!'):
+                        gc = gc[:-1]
+                        direction = 'r'
+                    else:
+                        direction = 'f'
+
+                    self.gene_synteny_data_dict[genome][contig][j] = {
+                        'gene_cluster_name': gc,
+                        'gene_cluster_id': '',
+                        'direction': direction,
+                        'rev_compd': 'False',
+                        'max_num_paralogs': 0
+                    }
+
+
+    def export_gene_synteny_to_yaml(self):
+
+        self.run.warning(None, header="Export the gene synteny to yaml file", lc="green")
+        gene_synteny_yaml_dict = {}
+        for genome in self.gene_synteny_data_dict.keys():
+            gene_synteny_yaml_dict[genome] = []
+            for contig in self.gene_synteny_data_dict[genome].keys():
+                contig_data = self.gene_synteny_data_dict[genome][contig]
+
+                contig_string = []
+
+                for gene_call in contig_data.keys():
+                    if contig_data[gene_call]['direction'] == 'f':
+                        contig_string += [contig_data[gene_call]['gene_cluster_name']]
+                    else:
+                        contig_string += [contig_data[gene_call]['gene_cluster_name'] + '!']
+
+                gene_synteny_yaml_dict[genome] += [' '.join(contig_string)]
+
+        utils.save_dict_as_yaml(gene_synteny_yaml_dict, self.output_yaml)
+
+        self.run.info_single("Done")
+
+
+    def get_gene_synteny_data_dict(self):
+        """A function to reduce a comprehensive data structure from anvi'o artifacts for
+           downstream analyses.
+        """
+        self.run.warning(None, header="Loading data from database", lc="green")
+
+        filesnpaths.is_file_tab_delimited(self.external_genomes_txt)
+
+        if not utils.is_all_columns_present_in_TAB_delim_file(["name","contigs_db_path"], self.external_genomes_txt):
+            raise ConfigError("Your external genomes file does not seem to contain that anvi'o expects to find "
+                              "in an external genomes file :/")
+
+        pan_db = dbops.PanSuperclass(self.args, r=terminal.Run(verbose=False), p=terminal.Progress(verbose=False))
+
+        self.project_name = pan_db.p_meta['project_name']
+
+        pan_db.init_gene_clusters()
+        pan_db.init_gene_clusters_functions_summary_dict()
+        pan_db.init_items_additional_data()
+
+        gene_cluster_dict = pan_db.gene_callers_id_to_gene_cluster
+        additional_info_cluster = pan_db.items_additional_data_dict
+
+        external_genomes = pd.read_csv(self.external_genomes_txt, header=0, sep="\t", names=["name","contigs_db_path"])
+        external_genomes.set_index("name", inplace=True)
+
+        for genome, contigs_db_path in external_genomes.iterrows():
+
+            if genome in self.genomes_names or not self.genomes_names:
+
+                self.genomes.append(genome)
+
+                args = argparse.Namespace(contigs_db=contigs_db_path.item())
+                contigs_db = dbops.ContigsSuperclass(args, r=terminal.Run(verbose=False), p=terminal.Progress(verbose=False))
+
+                caller_id_cluster = gene_cluster_dict[genome]
+                caller_id_cluster_df = pd.DataFrame.from_dict(caller_id_cluster, orient="index", columns=["gene_cluster_name"]).rename_axis("gene_caller_id").reset_index()
+                caller_id_cluster_df["gene_cluster_id"] = ""
+
+                contigs_db.init_functions()
+                gene_function_calls_df = pd.DataFrame.from_dict(contigs_db.gene_function_calls_dict, orient="index").rename_axis("gene_caller_id").reset_index()
+
+                all_gene_calls = caller_id_cluster_df['gene_caller_id'].values.tolist()
+                genes_in_contigs_df = pd.DataFrame.from_dict(contigs_db.get_sequences_for_gene_callers_ids(all_gene_calls, include_aa_sequences=True, simple_headers=True)[1], orient="index").rename_axis("gene_caller_id").reset_index()
+                additional_info_df = pd.DataFrame.from_dict(additional_info_cluster, orient="index").rename_axis("gene_cluster_name").reset_index()
+                additional_info_df.rename(columns={entry: entry + "_known" for entry in self.functional_annotation_sources_available}, inplace=True)
+
+                joined_contigs_df = caller_id_cluster_df.merge(genes_in_contigs_df, on="gene_caller_id", how="left").merge(gene_function_calls_df, on="gene_caller_id", how="left").merge(additional_info_df, on="gene_cluster_name", how="left")
+
+                if genome in self.genomes_reverse:
+                    joined_contigs_df.sort_values(["contig", "start", "stop"], axis=0, ascending=True, inplace=True)
+                else:
+                    joined_contigs_df.sort_values(["contig", "start", "stop"], axis=0, ascending=False, inplace=True)
+
+                joined_contigs_df.set_index(["contig", "gene_caller_id"], inplace=True)
+
+                self.gene_synteny_data_dict[genome] = joined_contigs_df.fillna("None").groupby(level=0).apply(lambda df: df.xs(df.name).to_dict("index")).to_dict()
+
+                self.run.info_single(f"Loaded genome {genome}.")
+
+            else:
+                self.run.info_single(f"Skipped genome {genome}.")
+
+        if not self.genomes:
+            raise ConfigError(f"Please keep at least one genome in the dataset. With the current setting you skip over all.")
+        else:
+            if not self.genomes_names:
+                self.genomes_names = self.genomes
+
+        self.run.info_single("Done")
+
+
+    def context_distance(self, a, b):
+        r_val = 0
+        f_val = 0
+        div = len(a)
+
+        if not a[int(len(a) / 2)] == b[int(len(b) / 2)]: 
+            raise ConfigError(f"This is very weird and should not have happend, we are very sorry :(.")
+
+        if set(self.genome_gc_occurence[tuple(a)].keys()).isdisjoint(set(self.genome_gc_occurence[tuple(b)].keys())):
+            for i, (n, m) in enumerate(zip(a, b)):
+
+                if not i == int(len(a) / 2):
+                    if (n[0] == '-' and m[0] == '-') or (n[0] == '+' and m[0] == '+'):
+                        if n[1] != m[1]:
+                            r_val += 0.5
+                    elif n[0] == '-' or m[0] == '-' or n[0] == '+' or m[0] == '+':
+                        r_val += 0
+                    elif n == m:
+                        r_val += 1
+
+            for i, (n, m) in enumerate(zip(a, b[::-1])):
+
+                if not i == int(len(a) / 2):
+                    if (n[0] == '-' and m[0] == '-') or (n[0] == '+' and m[0] == '+'):
+                        if n[1] != m[1]:
+                            f_val += 0.5
+                    elif n[0] == '-' or m[0] == '-' or n[0] == '+' or m[0] == '+':
+                        f_val += 0
+                    elif n == m:
+                        f_val += 1
+
+            if r_val >= f_val:
+                return (1 - r_val / div)
+            else:
+                return (1 - f_val / div)
+
+        elif tuple(a) == tuple(b):
+            return (0)
+
+        else:
+            return (1)
+
+
+    def context_split(self, label, gcp):
+
+        if len(label) == 1:
+            result = list(zip(label, [1]))
+            return (result)
+
+        else:
+            X = cdist(np.asarray(label), np.asarray(label), metric=self.context_distance)
+            condensed_X = squareform(X)
+
+            Z = linkage(condensed_X, 'ward')
+
+            for t in sorted(set(sum(Z.tolist(), [])), reverse=True):
+                clusters = fcluster(Z, t, criterion='distance')
+
+                valid = True
+                for c in set(clusters.tolist()):
+                    pos = np.where(clusters == c)[0]
+
+                    for i, j in it.combinations(pos, 2):
+
+                        if X[i][j] == 1.:
+                            valid = False
+
+                if valid is True:
+                    break
+
+            result = list(zip(label, clusters))
+
+            if self.output_graphics:
+                fig = plt.figure(figsize=(25, 10))
+                ax = plt.axes()
+                dn = dendrogram(Z, ax=ax, labels=label, orientation='right')
+                ax.axvline(linestyle='--', x=t)
+                plt.tight_layout()
+                fig.savefig(self.output_graphics + gcp + '.pdf')
+
+            return (result)
+
+
+    def run_contextualize_paralogs_algorithm(self):
+        """A function that resolves the graph context of paralogs based on gene synteny information across genomes"""
+        self.run.warning(None, header="Select paralog context", lc="green")
+
+        unresolved = True
+        solved = set()
+
+        genome_gc_order_values = {}
+        genome_gc_order_left_placeholder = {}
+        genome_gc_order_right_placeholder = {}
+
+        while unresolved:
+
+            unresolved = False
+            drop = set()
+
+            for genome in self.gene_synteny_data_dict.keys():
+                for contig in self.gene_synteny_data_dict[genome].keys():
+                    genome_gc_order = [self.gene_synteny_data_dict[genome][contig][gene_call]["gene_cluster_name"] for gene_call in self.gene_synteny_data_dict[genome][contig].keys()]
+
+                    if self.k == 0:
+                        if genome not in genome_gc_order_values:
+                            genome_gc_order_values[genome] = {contig: genome_gc_order}
+                            genome_gc_order_left_placeholder[genome] = {contig: '-0'}
+                            genome_gc_order_right_placeholder[genome] = {contig: '+0'}
+                        else:
+                            items = list(genome_gc_order_values[genome].values())
+                            times = items.count(genome_gc_order)
+                            if times == 0:
+                                genome_gc_order_values[genome][contig] = genome_gc_order
+                                genome_gc_order_left_placeholder[genome][contig] = '-0'
+                                genome_gc_order_right_placeholder[genome][contig] = '+0'
+                            else:
+                                genome_gc_order_values[genome][contig] = genome_gc_order
+                                genome_gc_order_left_placeholder[genome][contig] = '-' + chr(ord('a')+times-1)
+                                genome_gc_order_right_placeholder[genome][contig] = '+' + chr(ord('a')+times-1)
+
+                    left_place = genome_gc_order_left_placeholder[genome][contig]
+                    right_place = genome_gc_order_right_placeholder[genome][contig]
+
+                    for i in range(0, len(genome_gc_order)):
+
+                        start = (i - self.k) if (i - self.k) >= 0 else 0
+                        stop = (i + self.k + 1) if (i + self.k + 1) <= len(genome_gc_order) else len(genome_gc_order)
+                        entry = genome_gc_order[start:stop]
+
+                        if len(entry) == 1 + (2 * self.k):
+                            gc_k = tuple(entry)
+                        elif start == 0 and stop == len(genome_gc_order):
+                            gc_k = tuple([left_place] * (self.k - i) + entry + [right_place] * ((i + self.k + 1) - len(genome_gc_order)))
+                        elif start == 0:
+                            gc_k = tuple([left_place] * (self.k - i) + entry)
+                        elif stop == len(genome_gc_order):
+                            gc_k = tuple(entry + [right_place] * ((i + self.k + 1) - len(genome_gc_order)))
+                        else:
+                            raise ConfigError(f"The search frame of entry {entry} is malformed. It is not tuple of size {1 + (2 * self.k)}"
+                                              f"neiter is the frame overlapping with the beginning and the end of a very short contig"
+                                              f"nor with either of those. This is weird and should not happen, please check your input data"
+                                              f"and make sure there is nothing very weird going on there. Sorry :/")
+
+                        if len(gc_k) != 1 + (2 * self.k):
+                            raise ConfigError(f"Wow, for some unforseeable reason the length of the search frame is not matching the"
+                                              f"current iterration. I thought this is impossible and I'm very curious on how you accomplished"
+                                              f"that. Jokes aside errors can happen and I probably forgot some specific exception. Sorry...")
+
+                        gc = gc_k[int(len(gc_k) / 2)]
+                        if gc not in solved:
+
+                            if gc_k not in self.genome_gc_occurence.keys():
+                                self.genome_gc_occurence[gc_k] = {genome: 1}
+
+                            else:
+                                if genome not in self.genome_gc_occurence[gc_k].keys():
+                                    self.genome_gc_occurence[gc_k][genome] = 1
+                                else:
+                                    self.genome_gc_occurence[gc_k][genome] += 1
+
+            for gc, genome_gc_frequency in self.genome_gc_occurence.items():
+                if max(genome_gc_frequency.values()) > 1:
+
+                    unresolved = True
+                    drop.add(gc[int(len(gc)/2)])
+
+                elif self.k == 0 and len(genome_gc_frequency) == len(self.genomes):
+                    self.single_copy_core.add(gc)
+
+            if self.k == 0:
+                self.paralog_dict = copy.deepcopy(self.genome_gc_occurence)
+
+            if unresolved:
+                keys = list(self.genome_gc_occurence.keys())
+                for gc in keys:
+                    if gc[int(len(gc)/2)] in drop:
+                        self.genome_gc_occurence.pop(gc)
+
+                solved = set([gc[int(len(gc)/2)] for gc in self.genome_gc_occurence.keys()])
+                self.k += 1
+
+        g_cleaned = {}
+        gcs = set([gc[int(len(gc)/2)] for gc in self.genome_gc_occurence.keys()])
+
+        for gcp in gcs:
+            label = [gc for gc in self.genome_gc_occurence.keys() if gc[int(len(gc)/2)] == gcp]
+            context = self.context_split(label, gcp)
+
+            for name, cluster in context:
+                g_cleaned[name] = gcp + '_' + str(cluster)
+
+        self.run.info_single(f"{pp(self.k+1)} iteration(s) to expand {pp(len(self.paralog_dict.keys()))} GCs to {pp(len(self.genome_gc_occurence.keys()))} GCs without paralogs")
+        syn_calls = 0
+
+        for genome in self.gene_synteny_data_dict.keys():
+
+            for contig in self.gene_synteny_data_dict[genome].keys():
+                genome_gc_order = [(self.gene_synteny_data_dict[genome][contig][gene_call]["gene_cluster_name"], gene_call) for gene_call in self.gene_synteny_data_dict[genome][contig].keys()]
+
+                left_place = genome_gc_order_left_placeholder[genome][contig]
+                right_place = genome_gc_order_right_placeholder[genome][contig]
+
+                for i in range(0, len(genome_gc_order)):
+                    start = i-self.k if i-self.k >= 0 else 0
+                    stop = i+self.k+1 if i+self.k+1 <= len(genome_gc_order) else len(genome_gc_order)
+                    entry = [item[0] for item in genome_gc_order[start:stop]]
+                    gene_call = genome_gc_order[i][1]
+                    name = genome_gc_order[i][0]
+
+                    if len(entry) == 1 + (2 * self.k):
+                        gc_k = tuple(entry)
+                    elif start == 0 and stop == len(genome_gc_order):
+                        gc_k = tuple([left_place] * (self.k - i) + entry + [right_place] * ((i + self.k + 1) - len(genome_gc_order)))
+                    elif start == 0:
+                        gc_k = tuple([left_place] * (self.k - i) + entry)
+                    elif stop == len(genome_gc_order):
+                        gc_k = tuple(entry + [right_place] * ((i + self.k + 1) - len(genome_gc_order)))
+                    else:
+                        raise ConfigError(f"The search frame of entry {entry} is malformed. It is not tuple of size {1 + (2 * self.k)}"
+                                          f"neiter is the frame overlapping with the beginning and the end of a very short contig"
+                                          f"nor with either of those. This is weird and should not happen, please check your input data"
+                                          f"and make sure there is nothing very weird going on there. Sorry :/")
+
+                    for j in range(0, self.k+1):
+
+                        gc_group = gc_k[int(len(gc_k)/2)-j:int(len(gc_k)/2)+j+1]
+
+                        if gc_group in self.genome_gc_occurence.keys():
+
+                            self.gene_synteny_data_dict[genome][contig][gene_call]["gene_cluster_id"] = g_cleaned[gc_group]
+                            syn_calls += 1
+                            break
+
+                        else:
+                            pass
+
+        num_calls = 0
+        for _, value in self.genome_gc_occurence.items():
+            num_calls += sum(value.values())
+
+        if num_calls != syn_calls:
+            raise ConfigError(f"It looks like {abs(num_calls - syn_calls)} calls were not  captured by the algorithm. Proceeding from"
+                              f"here is a very bad idea. We will try to do better next time. For now please check your data to make"
+                              f"sure you did not try some very crazy stuff.")
+
+        self.run.info_single("Done")
+
+
+    def add_node_to_graph(self, gene_cluster, name, info):
+
+        if not self.initial_graph.has_node(gene_cluster):
+            self.initial_graph.add_node(
+                gene_cluster,
+                name=name,
+                pos=(0, 0),
+                weight=1,
+                layer={},
+                genome=info
+            )
+
+        else:
+            self.initial_graph.nodes[gene_cluster]['weight'] += 1
+            self.initial_graph.nodes[gene_cluster]['genome'].update(info)
+
+
+    def add_edge_to_graph(self, gene_cluster_i, gene_cluster_j, info):
+
+        if self.priority_genome in info.keys():
+            weight_add = 100
+        elif gene_cluster_i in self.single_copy_core and gene_cluster_j in self.single_copy_core:
+            weight_add = 2
+        elif gene_cluster_i in self.single_copy_core or gene_cluster_j in self.single_copy_core:
+            weight_add = 1
+        else:
+            weight_add = 0
+
+        draw = {genome: {'gene_call': -1} for genome in info.keys()}
+
+        if not self.initial_graph.has_edge(*(gene_cluster_i, gene_cluster_j)):
+            self.initial_graph.add_edge(
+                *(gene_cluster_i, gene_cluster_j),
+                weight=1 + weight_add,
+                genome=draw,
+                bended=[],
+                direction='R'
+            )
+
+        else:
+            self.initial_graph[gene_cluster_i][gene_cluster_j]['weight'] += 1 + weight_add
+            self.initial_graph[gene_cluster_i][gene_cluster_j]['genome'].update(draw)
+
+
+    def build_graph(self):
+
+        self.run.warning(None, header="Building directed gene cluster graph G", lc="green")
+
+        for genome in self.gene_synteny_data_dict.keys():
+
+            for contig in self.gene_synteny_data_dict[genome].keys():
+                gene_cluster_kmer = []
+                for gene_call in self.gene_synteny_data_dict[genome][contig].keys():
+                    gene_cluster_kmer.append((self.gene_synteny_data_dict[genome][contig][gene_call]['gene_cluster_id'], self.gene_synteny_data_dict[genome][contig][gene_call]['gene_cluster_name'], {genome: {'contig':contig, 'gene_call':gene_call, **self.gene_synteny_data_dict[genome][contig][gene_call]}}))
+
+                if len(gene_cluster_kmer) > 1:
+                    gene_cluster_pairs = map(tuple, zip(gene_cluster_kmer, gene_cluster_kmer[1:]))
+                    first_pair = next(gene_cluster_pairs)
+
+                    self.add_node_to_graph(first_pair[0][0], first_pair[0][1], first_pair[0][2])
+                    self.add_node_to_graph(first_pair[1][0], first_pair[1][1], first_pair[1][2])
+                    self.add_edge_to_graph(first_pair[0][0], first_pair[1][0], first_pair[1][2])
+
+                    for gene_cluster_pair in gene_cluster_pairs:
+
+                        self.add_node_to_graph(gene_cluster_pair[1][0], gene_cluster_pair[1][1], gene_cluster_pair[1][2])
+                        self.add_edge_to_graph(gene_cluster_pair[0][0], gene_cluster_pair[1][0], gene_cluster_pair[1][2])
+
+                else:
+                    self.add_node_to_graph(gene_cluster_kmer[0][0], gene_cluster_kmer[0][1], gene_cluster_kmer[0][2])
+
+        self.run.info_single(f"Adding {pp(len(self.initial_graph.nodes()))} nodes and {pp(len(self.initial_graph.edges()))} edges to G")
+
+        if self.pass_filter == 0:
+            self.run.info_single("Setting algorithm to 'no pass filter'")
+        else:
+            self.run.info_single(f"Setting algorithm to 'remove edges < {pp(self.pass_filter)}'")
+
+        edges_to_remove = [(i, j) for i,j,k in self.initial_graph.edges(data=True) if k['weight'] < self.pass_filter]
+
+        self.run.info_single(f"Removed {pp(len(edges_to_remove))} edges due to pass filter.")
+
+        self.initial_graph.remove_edges_from(edges_to_remove)
+
+        connectivity = nx.is_connected(self.initial_graph.to_undirected())
+        self.run.info_single(f"Connectivity is {connectivity}")
+
+        if connectivity == False:
+
+            weakly_components = list(nx.weakly_connected_components(self.initial_graph))
+            self.run.info_single(f"Graph contains {pp(len(weakly_components))} independant components.")
+
+            self.pangenome_graph = nx.DiGraph(self.initial_graph.subgraph(max(weakly_components, key=len)))
+            self.run.info_single(f"Keeping longest subgraph with {pp(len(self.pangenome_graph.nodes()))} nodes and {pp(len(self.pangenome_graph.edges()))} edges")
+
+            connectivity = nx.is_connected(self.pangenome_graph.to_undirected())
+            self.run.info_single(f"Connectivity is {connectivity}")
+        else:
+            self.pangenome_graph = nx.DiGraph(self.initial_graph)
+
+        self.run.info_single("Done")
+        self.run.warning(None, header="Building maximum branching graph M of G", lc="green")
+
+        selfloops = list(nx.selfloop_edges(self.pangenome_graph))
+        self.run.info_single(f"Found and removed {pp(len(selfloops))} selfloop edge(s)")
+        self.pangenome_graph.remove_edges_from(selfloops)
+
+        edmonds = nx.algorithms.tree.branchings.Edmonds(self.pangenome_graph)
+        self.edmonds_graph = edmonds.find_optimum(
+            attr="weight",
+            default=1,
+            kind="max",
+            style="arborescence",
+            preserve_attrs=False,
+            partition=None,
+        )
+
+        if not nx.algorithms.tree.recognition.is_arborescence(self.edmonds_graph):
+            self.run.info_single('No maximum aborescence. Entering fallback mode.')
+            edmonds_sub_graph = max(nx.weakly_connected_components(self.edmonds_graph), key=len)
+            self.edmonds_graph = nx.DiGraph(self.edmonds_graph.subgraph(edmonds_sub_graph))
+            self.pangenome_graph = nx.DiGraph(self.pangenome_graph.subgraph(edmonds_sub_graph))
+            if nx.algorithms.tree.recognition.is_arborescence(self.edmonds_graph):
+                self.run.info_single('Found aborescence.')
+
+                #TODO calculate number of missing edges
+                self.run.info_single(f'{len(self.edmonds_graph.nodes())-len(edmonds_sub_graph)} nodes removed to capture synteny.')
+                self.run.info_single('Be warned the quality of the pangraph might have suffered.')
+                self.run.info_single('Proceed.')
+            else:
+                raise ConfigError(f"I'm very sorry to inform you that your data is not solvable by the current version of"
+                                  f"anvi'o pangraph. The fallback mode tried to solve your dataset by sacrificing some"
+                                  f"of the included information, but at this scale it will not lead to a acceptable result :(")
+
+        else:
+            self.run.info_single('Found aborescence. Proceed.')
+
+        nx.set_edge_attributes(self.edmonds_graph, {(i, j): d for i, j, d in self.pangenome_graph.edges(data=True) if (i, j) in self.edmonds_graph.edges()})
+        nx.set_node_attributes(self.edmonds_graph, {k: d for k, d in self.pangenome_graph.nodes(data=True) if k in self.edmonds_graph.nodes()})
+
+        add_start = []
+        for node in self.edmonds_graph.nodes():
+            if len(list(self.edmonds_graph.predecessors(node))) == 0:
+                add_start.append(node)
+
+        for graph in [self.pangenome_graph, self.edmonds_graph]:
+            graph.add_node(
+                'start',
+                name='start',
+                pos=(0, 0),
+                weight=len(self.genomes),
+                layer={},
+                genome={genome: {'gene_call': -1, 'contig': '', 'direction': ''} for genome in self.genomes}
+            )
+
+            for u in add_start:
+
+                weight = graph.nodes[u]['weight']
+                genomes = graph.nodes[u]['genome'].keys()
+
+                graph.add_edge(
+                    *('start', u),
+                    genome={genome: {'gene_call': -1} for genome in genomes},
+                    weight=weight,
+                    bended=[],
+                    direction='R'
+                )
+
+        self.run.info_single(f"Removing {pp(len(self.pangenome_graph.edges()) - len(self.edmonds_graph.edges()))} edges from G to create M")
+        self.run.info_single("Done")
+
+    def find_next_branching_point(self, current):
+        if current != 'start':
+            pred = list(self.edmonds_graph.predecessors(current))[0]
+            pred_successors = list(self.edmonds_graph.successors(pred))
+            if len(pred_successors) > 1:
+                return(pred)
+            else:
+                self.find_next_branching_point(pred)
+
+
+    def mean_edmonds_graph_path_weight(self, source, target):
+        path = nx.shortest_path(G=self.edmonds_graph, source=source, target=target, weight='weight')
+        path_weight = nx.path_weight(G=self.edmonds_graph, path=path, weight='weight')
+        return(path_weight)
+
+
+    def get_edge(self, node_i, node_j, reverse = False):
+
+        if reverse == False:
+            pangenome_graph_edge_data = self.pangenome_graph.get_edge_data(node_i, node_j)
+            return(node_i, node_j, pangenome_graph_edge_data)
+        else:
+            pangenome_graph_edge_data = {y:z if y != 'direction' else 'L' for y,z in self.pangenome_graph.get_edge_data(node_i, node_j).items()}
+            return(node_j, node_i, pangenome_graph_edge_data)
+
+
+    def get_leaves(self, current_branch_successor, edmonds_graph_successors):
+        leaves = set()
+        while True:
+            successors = edmonds_graph_successors[current_branch_successor]
+
+            if successors:
+                if len(successors) > 1:
+                    for successor in successors:
+                        leaves.update(self.get_leaves(successor, edmonds_graph_successors))
+                    break
+                else:
+                    current_branch_successor = successors[0]
+            else:
+                leaves.update(set([current_branch_successor]))
+                break
+
+        return(leaves)
+
+
+    def edge_check(self, node_i, node_j, data):
+
+        new_data = copy.deepcopy(data)
+
+        if self.edmonds_graph.has_edge(node_i, node_j):
+            old_data = self.edmonds_graph[node_i][node_j]
+            new_data['genome'].update(old_data['genome'])
+            new_data['weight'] += old_data['weight']
+            new_data['direction'] = 'B'
+
+        return(new_data)
+
+
+    def run_tree_to_flow_network_algorithm(self):
+
+        self.run.warning(None, header="Building flow network F from M and G", lc="green")
+
+        edmonds_graph_edges = set(self.edmonds_graph.edges())
+        edmonds_graph_nodes = set(self.edmonds_graph.nodes())
+
+        pangenome_graph_edges = set(self.pangenome_graph.edges())
+        pangenome_graph_nodes = set(self.pangenome_graph.nodes())
+
+        edmonds_graph_removed_edges = pangenome_graph_edges - edmonds_graph_edges
+        edmonds_graph_end = max([(self.mean_edmonds_graph_path_weight('start', node), node) for node in edmonds_graph_nodes if len(list(self.edmonds_graph.successors(node))) == 0])[1]
+
+        for graph in [self.pangenome_graph, self.edmonds_graph]:
+
+            graph.add_node(
+                'stop',
+                name='stop',
+                pos=(0, 0),
+                weight=len(self.genomes),
+                layer={},
+                genome={genome: {'gene_call': -1, 'contig': '', 'direction': ''} for genome in self.genomes}
+            )
+            graph.add_edge(
+                *(edmonds_graph_end, 'stop'),
+                genome={genome: {'gene_call': -1} for genome in self.genomes},
+                weight=len(self.genomes),
+                bended=[],
+                direction='R'
+            )
+
+        edmonds_graph_nodes.add('stop')
+        edmonds_graph_predecessors = {edmonds_graph_node: list(self.edmonds_graph.predecessors(edmonds_graph_node))[0] for edmonds_graph_node in edmonds_graph_nodes if edmonds_graph_node != 'start'}
+        edmonds_graph_successors = {edmonds_graph_node: list(self.edmonds_graph.successors(edmonds_graph_node)) for edmonds_graph_node in edmonds_graph_nodes}
+        pangenome_graph_successors = {pangenome_graph_node: list(self.pangenome_graph.successors(pangenome_graph_node)) for pangenome_graph_node in pangenome_graph_nodes}
+        edmonds_graph_distances = {edmonds_graph_node: self.mean_edmonds_graph_path_weight('start', edmonds_graph_node) for edmonds_graph_node in edmonds_graph_nodes}
+
+        i = 0
+        resolved_nodes = set(['stop'])
+
+        pred = ''
+        x = 0
+        self.progress.new("Solving complex graph")
+        while len(resolved_nodes) != len(pangenome_graph_nodes) + 1 or x < 1:
+            if len(resolved_nodes) == len(pangenome_graph_nodes) + 1:
+                x += 1
+
+            i += 1
+
+            visited_nodes = set(['stop'])
+            current_node = 'stop'
+            while len(visited_nodes) != len(pangenome_graph_nodes) + 1:
+
+                self.progress.update(f"{str(len(resolved_nodes)).rjust(len(str(len(pangenome_graph_nodes) + 1)), ' ')} / {len(pangenome_graph_nodes) + 1}")
+
+                if pred:
+                    current_branch_root = pred
+                    pred = ''
+                else:
+                    current_branch_root = edmonds_graph_predecessors[current_node]
+
+                current_forward_connected = []
+                current_backward_connected = []
+                successor_branch_leaves = set()
+
+                for current_branch_successor in edmonds_graph_successors[current_branch_root]:
+                    if current_branch_successor not in visited_nodes and current_branch_successor != current_node:
+                        successor_branch_leaves.update(self.get_leaves(current_branch_successor, edmonds_graph_successors))
+
+                if not successor_branch_leaves:
+                    current_node = current_branch_root
+                else:
+                    current_node = max([(edmonds_graph_distances[successor_branch_leaf], successor_branch_leaf) for successor_branch_leaf in successor_branch_leaves])[1]
+
+                if current_node in resolved_nodes:
+                    connected = True
+                else:
+                    connected = False
+
+                if connected != True or x == 1:
+                    for current_node_successor in pangenome_graph_successors[current_node]:
+
+                        if current_node_successor in resolved_nodes:
+
+                            if current_node_successor in nx.ancestors(self.edmonds_graph, current_node) or (current_node_successor not in visited_nodes and current_node_successor not in resolved_nodes):
+                                if (current_node, current_node_successor) in edmonds_graph_removed_edges:
+                                    current_backward_connected.append(current_node_successor)
+
+                            else:
+                                if (current_node, current_node_successor) in edmonds_graph_removed_edges:
+                                    current_forward_connected.append(current_node_successor)
+                                    connected = True
+
+                                else:
+                                    connected = True
+
+                    if connected == False:
+                        if len(list(self.pangenome_graph.successors(current_node))) == 0:
+                            pangenome_graph_edge_data = {
+                                'genome':{genome: {'gene_call': -1} for genome in self.genomes},
+                                'weight':len(self.genomes),
+                                'bended': [],
+                                'direction': 'R'
+                            }
+
+                            new_data = self.edge_check(current_node, 'stop', pangenome_graph_edge_data)
+                            self.edmonds_graph.add_edge(current_node, 'stop', **new_data)
+                            connected = True
+
+                    if connected == True:
+                        for current_forward in current_forward_connected:
+                            node_i, node_j, data = self.get_edge(current_node, current_forward, reverse = False)
+
+                            new_data = self.edge_check(node_i, node_j, data)
+                            self.edmonds_graph.add_edge(node_i, node_j, **new_data)
+                            edmonds_graph_removed_edges.remove((current_node, current_forward))
+
+                        for current_backward in current_backward_connected:
+                            node_i, node_j, data = self.get_edge(current_node, current_backward, reverse = True)
+
+                            new_data = self.edge_check(node_i, node_j, data)
+                            self.edmonds_graph.add_edge(node_i, node_j, **new_data)
+                            edmonds_graph_removed_edges.remove((current_node, current_backward))
+
+                        resolved_nodes.add(current_node)
+
+                    else:
+                        if current_backward_connected:
+
+                            number = max([(self.pangenome_graph.get_edge_data(current_node, backward)['weight'], i) for (i, backward) in enumerate(current_backward_connected)])[1]
+
+                            node_i, node_j, data = self.get_edge(current_node, current_backward_connected[number], reverse = True)
+                            self.edmonds_graph.remove_edge(edmonds_graph_predecessors[current_node], current_node)
+
+                            new_data = self.edge_check(node_i, node_j, data)
+                            self.edmonds_graph.add_edge(node_i, node_j, **new_data)
+
+                            edmonds_graph_removed_edges.remove((current_node, current_backward_connected[number]))
+                            edmonds_graph_removed_edges.add((edmonds_graph_predecessors[current_node], current_node))
+
+                            edmonds_graph_successors[edmonds_graph_predecessors[current_node]].remove(current_node)
+                            edmonds_graph_successors[current_backward_connected[number]] += [current_node]
+
+                            pred = edmonds_graph_predecessors[current_node]
+
+                            edmonds_graph_predecessors.pop(current_node, None)
+                            edmonds_graph_predecessors[current_node] = current_backward_connected[number]
+
+                            edmonds_graph_distances[current_node] = self.mean_edmonds_graph_path_weight('start', current_node)
+
+                            resolved_nodes.add(current_node)
+
+                visited_nodes.add(current_node)
+
+                if not nx.is_directed_acyclic_graph(self.edmonds_graph):
+                    raise ConfigError(f"Oh no. It looks like your graph is so complex or includes a motif I haven't seen before"
+                                      f"therefore the reattachement algorithm itself included a loop to the graph. We had multiple"
+                                      f"sanity checks to prevent this but unfortunatly nobody is perfect. We will include more"
+                                      f"checks in the next version. Sorry :/")
+
+        self.progress.end()
+
+        remaining_stops = [node for node in self.edmonds_graph.nodes() if self.edmonds_graph.out_degree(node) == 0 and node != 'stop']
+        self.run.info_single(f"{pp(i)} iterations to solve the graph")
+
+        for stop in remaining_stops:
+
+            pangenome_graph_edge_data = {
+                'genome':{genome: {'gene_call': -1} for genome in self.genomes},
+                'weight':len(self.genomes),
+                'bended': [],
+                'direction': 'R'
+            }
+
+            new_data = self.edge_check(stop, 'stop', pangenome_graph_edge_data)
+            self.edmonds_graph.add_edge(stop, 'stop', **new_data)
+
+            edmonds_graph_successors[stop] += ['stop']
+
+        if not nx.is_directed_acyclic_graph(self.edmonds_graph):
+            raise ConfigError(f"Oh no. It looks like your graph is so complex or includes a motif I haven't seen before"
+                              f"therefore the reattachement algorithm itself included a loop to the graph. We had multiple"
+                              f"sanity checks to prevent this but unfortunatly nobody is perfect. We will include more"
+                              f"checks in the next version. Sorry :/")
+
+        self.run.info_single("Done")
+
+
+    def load_graph_from_json_file(self):
+
+        self.run.warning(None, header="Import graph F from json file", lc="green")
+
+        filesnpaths.is_file_json_formatted(self.pan_graph_json)
+
+        self.jsondata = json.load(open(self.pan_graph_json))
+
+        self.global_x = int(self.jsondata["infos"]["meta"]["global_x"])
+        self.priority_genome = self.jsondata["infos"]["priority_genome"]
+
+        self.global_y = 0
+        self.ancest = nx.DiGraph()
+        self.x_list = {}
+        self.position = {}
+        self.edges = {}
+
+        for x in range(0, self.global_x+1):
+            self.x_list[x] = []
+
+        for node in self.jsondata["elements"]["nodes"]:
+            name = self.jsondata["elements"]["nodes"][node]["name"]
+            weight = self.jsondata["elements"]["nodes"][node]["weight"]
+            genome = self.jsondata["elements"]["nodes"][node]["genome"]
+            x = self.jsondata["elements"]["nodes"][node]["position"]["x"]
+
+            self.x_list[x].append(node)
+            self.position[node] = (x, -1)
+            self.ancest.add_node(node, name=name, pos=(0,0), weight=weight, layer={}, genome=genome)
+
+        for edge in self.jsondata["elements"]["edges"]:
+            source = self.jsondata["elements"]["edges"][edge]["source"]
+            target = self.jsondata["elements"]["edges"][edge]["target"]
+            genome = self.jsondata["elements"]["edges"][edge]["genome"]
+            direction = self.jsondata["elements"]["edges"][edge]["direction"]
+
+            self.ancest.add_edge(source, target, weight=-1, genome=genome, bended=[], direction=direction)
+
+        self.run.info_single("Done")
+
+
+    def prepare_synteny_graph(self):
+
+        for x, generation in enumerate(nx.topological_generations(self.edmonds_graph)):
+            self.x_list[x] = generation
+            for node in generation:
+                self.position[node] = (x, -1)
+
+        self.global_x = x
+
+        self.ancest = nx.DiGraph(self.edmonds_graph)
+        nx.set_edge_attributes(self.ancest, values=-1, name='weight')
+
+
+    def run_synteny_layout_algorithm(self):
+
+        self.run.warning(None, header="Calculating coordinates on the nodes from F", lc="green")
+
+        layout_graph_nodes = list(self.ancest.nodes())
+        layout_graph_successors = {layout_graph_node: list(self.ancest.successors(layout_graph_node)) for layout_graph_node in layout_graph_nodes}
+
+        n_removed = 0
+        ghost = 0
+        for x in range(self.global_x-1, 0, -1):
+            for node in self.x_list[x]:
+                node_x_position = self.position[node][0]
+
+                change = []
+                for successor in layout_graph_successors[node]:
+                    if successor != 'stop':
+                        successor_x_position = self.position[successor][0]
+
+                        if successor_x_position <= node_x_position:
+                            raise ConfigError(f"The node {node} is succeded by the node {successor} which is in front of the node {node}"
+                                              f"that does not make a lot of sense and should not happen. We are sorry for the inconvenience :/")
+                        else:
+                            change.append((successor_x_position, successor))
+
+                if change:
+                    if min(change)[0] > 1:
+                        new_x_position = min([(x, n) for (x, n) in change if x > 1])[0] - 1
+                        self.position[node] = (new_x_position, -1)
+
+                    for (position, extend_successor) in change:
+                        x_difference = position - new_x_position
+
+                        if x_difference <= self.max_edge_length_filter or self.max_edge_length_filter == -1:
+
+                            path_list = [node]
+
+                            for i in range(1, x_difference):
+                                path_list += ['Ghost_' + str(ghost)]
+                                self.position['Ghost_' + str(ghost)] = (new_x_position + i, -1)
+                                ghost += 1
+
+                            path_list += [extend_successor]
+
+                            self.edges[(node, extend_successor)] = (path_list, self.ancest.edges[node, extend_successor])
+                            self.ancest.remove_edge(node, extend_successor)
+
+                            if len(path_list) == 2:
+                                self.ancest.add_edges_from(map(tuple, zip(path_list, path_list[1:])), weight=-1)
+                            else:
+                                self.ancest.add_edges_from(map(tuple, zip(path_list, path_list[1:])), weight=-0.5)
+
+                        else:
+                            n_removed += 1
+                            self.removed.add((node, extend_successor))
+
+        for i, j in self.ancest.edges():
+
+            if self.position[j][0] - self.position[i][0] != 1 and i != 'start' and j != 'stop' and (i,j) not in self.removed:
+                raise ConfigError(f"Hmmm. This situation would create a very weird looking connection."
+                                  f"The ede {(i, j)} is longer than it should be. I don't know what created"
+                                  f"this but we will work on a solution on the next release. Sorry :(")
+
+        if self.max_edge_length_filter == -1:
+            self.run.info_single("Setting algorithm to 'keep all edges'")
+        else:
+            self.run.info_single(f"Setting algorithm to 'max edge length < {pp(self.max_edge_length_filter)}'")
+
+        self.run.info_single(f"Removed {pp(n_removed)} edge(s) due to length cutoff")
+
+        longest_path = nx.bellman_ford_path(G=self.ancest, source='start', target='stop', weight='weight')
+        m = set(longest_path)
+
+        starts = [node for node in self.ancest.nodes() if self.ancest.in_degree(node) == 0 if node != 'start']
+        for st in starts:
+            self.ancest.add_edge('start', st, weight=-1)
+        dfs_list = list(nx.dfs_edges(self.ancest, source='start'))
+
+        group = 0
+        groups = {}
+        groups_rev = {}
+
+        # TODO Currently no seperation between unequal genome context
+        if self.gene_cluster_grouping_threshold == -1:
+            self.run.info_single("Setting algorithm to 'no grouping'")
+        else:
+            self.run.info_single(f"Setting algorithm to 'Grouping single connected chains size > {pp(self.gene_cluster_grouping_threshold)}'")
+
+        for node_v, node_w in dfs_list:
+            if node_v != 'start' and self.ancest.in_degree(node_v) == 1 and self.ancest.out_degree(node_v) == 1 and self.ancest.in_degree(node_w) == 1 and self.ancest.out_degree(node_w) == 1:
+                
+                if self.ungroup[0] != -1 and self.ungroup[1] != -1 and self.position[node_v][0] > self.ungroup[0] and self.position[node_v][0] < self.ungroup[1] and self.position[node_w][0] > self.ungroup[0] and self.position[node_w][0] < self.ungroup[1]:
+                    continue
+                else:
+                    if node_v not in groups_rev.keys():
+                        group_name = 'GCG_' + str(group).zfill(8)
+                        groups[group_name] = [node_v, node_w]
+                        groups_rev[node_v] = group_name
+                        groups_rev[node_w] = group_name
+                        group += 1
+
+                    else:
+                        group_name = groups_rev[node_v]
+                        groups[group_name] += [node_w]
+                        groups_rev[node_w] = group_name
+
+        for label, condense_nodes in groups.items():
+
+            condense_nodes = [node for node in condense_nodes if not node.startswith('Ghost_')]
+
+            if len(condense_nodes) >= self.gene_cluster_grouping_threshold and self.gene_cluster_grouping_threshold != -1:
+                self.grouping[label] = condense_nodes
+
+        self.run.info_single(f"Grouped {pp(len(sum(self.grouping.values(), [])))} nodes in {pp(len(self.grouping.keys()))} groups")
+
+        for st in starts:
+            self.ancest.remove_edge('start', st)
+
+        self.ancest.remove_edges_from(self.removed)
+
+        branches = {}
+        sortable = []
+        for g in groups.keys():
+            branch = groups[g]
+
+            if not set(branch).isdisjoint(m) and not set(branch).issubset(m):
+                raise ConfigError(f"A group is neither disjoint from the main path nor subset of the main path"
+                                  f"we should not continue from here as this is not something that should happen.")
+                # print('Sanity Error. Code 10.')
+                # break
+
+            elif set(branch).isdisjoint(m):
+
+                start = self.position[branch[0]][0]
+                length = len(branch)
+
+                if start in branches.keys():
+                    if length in branches[start].keys():
+                        if branches[start][length].keys():
+                            num = max(branches[start][length].keys()) + 1
+                        else:
+                            num = 1
+
+                        branches[start][length][num] = branch
+                    else:
+                        num = 1
+                        branches[start][length] = {num: branch}
+                else:
+                    num = 1
+                    branches[start] = {length: {num: branch}}
+
+                sortable += [(start, length, num)]
+
+        left_nodes = set(self.ancest.nodes()) - set(groups_rev.keys())
+        for n in left_nodes:
+
+            if not set([n]).isdisjoint(m) and not set([n]).issubset(m):
+                raise ConfigError(f"A group is neither disjoint from the main path nor subset of the main path"
+                                  f"we should not continue from here as this is not something that should happen.")
+                # print('Sanity Error. Code 11.')
+                # break
+
+            elif set([n]).isdisjoint(m):
+                start = self.position[n][0]
+                length = 1
+                if n != 'start' and n != 'stop':
+                    if start in branches.keys():
+                        if length in branches[start].keys():
+                            if branches[start][length].keys():
+                                num = max(branches[start][length].keys()) + 1
+                            else:
+                                num = 1
+
+                            branches[start][length][num] = [n]
+                        else:
+                            num = 1
+                            branches[start][length] = {num: [n]}
+                    else:
+                        num = 1
+                        branches[start] = {length: {num: [n]}}
+
+                    sortable += [(start, length, num)]
+
+        used = set()
+        finished = set()
+
+        y_new = 0
+        for node in longest_path:
+            x_pos = self.position[node][0]
+            self.position[node] = (x_pos, y_new)
+            used.add((x_pos, y_new))
+            finished.add(node)
+
+        stack = [longest_path]
+        while stack:
+
+            current = stack[0]
+
+            remove = True
+            for i,j,k in sorted(sortable, key=lambda x: (x[1], x[0]), reverse = False):
+                branch = branches[i][j][k]
+                branch_pred = set(self.ancest.predecessors(branch[0]))
+                branch_succ = set(self.ancest.successors(branch[-1]))
+                if (not branch_pred.isdisjoint(set(current))) or (not branch_succ.isdisjoint(set(current))) or (not branch_pred.isdisjoint(set(current)) and not branch_succ.isdisjoint(set(current))):
+
+                    remove = False
+                    sortable.remove((i,j,k))
+                    y_new = max(sum([[self.position[ypred][1] for ypred in branch_pred], [self.position[ysucc][1] for ysucc in branch_succ]], []))
+
+                    stack = [branch] + stack
+                    while True:
+                        repeat = False
+                        for xnew in range(i, i+j):
+                            if (xnew, y_new) in used:
+                                repeat = True
+
+                        if repeat == False:
+                            break
+                        else:
+                            y_new += 1
+
+                    for node in branch:
+                        x_pos = self.position[node][0]
+                        self.position[node] = (x_pos, y_new)
+                        used.add((x_pos, y_new))
+                        finished.add(node)
+
+                        self.global_y = y_new if y_new > self.global_y else self.global_y
+
+                    break
+
+            if remove == True:
+                stack.remove(current)
+
+        if len(set(self.position.values())) != len(self.position.values()):
+            # print(len(self.position.values()) - len(set(self.position.values())))
+            raise ConfigError(f"No no no no. Something went very wrong here. Some nodes overlap in the UI."
+                              f"We don't want this, we definitely don't want this...")
+
+        for edge_i, edge_j in self.edges.keys():
+            path_list, infos = self.edges[(edge_i, edge_j)]
+
+            self.ancest.add_edge(edge_i, edge_j, **infos)
+            self.ancest[edge_i][edge_j]['weight'] = sum([1 if value != self.priority_genome else 10 for value in self.ancest[edge_i][edge_j]['genome'].keys()])
+            self.ancest[edge_i][edge_j]['bended'] = [self.position[p] for p in path_list[1:-1]]
+            self.ancest.remove_nodes_from(path_list[1:-1])
+
+        for node in self.ancest.nodes():
+            self.ancest.nodes[node]['pos'] = self.position[node]
+
+            self.offset[node] = self.position[node][0]
+
+        x_positions_list = []
+
+        for group_name in self.grouping.keys():
+
+            group = self.grouping[group_name]
+
+            group_size = len(group)
+            group_size_compressed = round(group_size * self.groupcompress)
+            compressed_factor = group_size_compressed if group_size_compressed == 0 else group_size_compressed - 1
+
+            node_distance_factor = compressed_factor / (group_size - 1)
+
+            start_x = self.ancest.nodes[group[0]]['pos'][0]
+
+            for i, node in enumerate(group):
+                self.offset[node] = round(start_x + i * node_distance_factor)
+
+            compressed_length = int(self.offset[group[-1]] - self.offset[group[0]])
+
+            x_positions_list += [i for i in range(start_x, start_x + compressed_length + 1)]
+
+        x_positions_list += list(self.offset.values())
+        x_positions = set(x_positions_list)
+        empty_spots = []
+
+        for x in range(self.global_x+1):
+            if x not in x_positions:
+                empty_spots.append(x)
+
+        for node in self.ancest.nodes():
+            decrease = 0
+            x = self.offset[node]
+            for e in empty_spots:
+                if x > e:
+                    decrease += 1
+
+                    if e == empty_spots[-1]:
+                        self.offset[node] = x - decrease
+                        break
+
+                else:
+                    self.offset[node] = x - decrease
+                    break
+
+        for edge_i, edge_j, data in self.ancest.edges(data=True):
+            if edge_i != 'start' and edge_j != 'stop':
+                if data['bended']:
+                    for i, (x, y) in enumerate(data['bended']):
+                        decrease = 0
+                        for e in empty_spots:
+                            if x > e-1:
+                                decrease += 1
+                            else:
+                                data['bended'][i] = (x - decrease, y)
+                                break
+                        else:
+                            data['bended'][i] = (x - decrease, y)
+
+                else:
+                    if self.offset[edge_j] - self.offset[edge_i] != 1:
+
+                        y = self.position[edge_i][1]
+                        x = self.offset[edge_i] + 1
+
+                        while x < self.offset[edge_j]:
+                            data['bended'].append((x, y))
+                            x += 1
+
+        self.global_x_offset = self.offset['stop']
+
+        self.run.info_single(f"Final graph {pp(len(self.ancest.nodes()))} nodes and {pp(len(self.ancest.edges()))} edges")
+        
+        self.run.info_single("Done")
+
+
+    def generate_data_table(self):
+
+        self.run.warning(None, header="Import layer values inherited from the pangenome", lc="green")
+
+        max_paralogs = 0
+
+        for gene_cluster in self.ancest.nodes():
+
+            if gene_cluster != 'start' and gene_cluster != 'stop':
+                node = self.ancest.nodes()[gene_cluster]
+                num = len(node['genome'].keys())
+                max_paralog_list = []
+                num_dir_r = 0
+                num_dir_l = 0
+
+                func_homogeneity_list = []
+                geo_homogeneity_list = []
+                comb_homogeneity_list = []
+
+                for genome in node['genome'].keys():
+                    info = node['genome'][genome]
+
+                    max_paralog_list.append(info['max_num_paralogs'])
+                    func_homogeneity_list.append(info['functional_homogeneity_index'])
+                    geo_homogeneity_list.append(info['geometric_homogeneity_index'])
+                    comb_homogeneity_list.append(info['combined_homogeneity_index'])
+
+                    if info['direction'] == 'r':
+                        num_dir_r += 1
+                    else:
+                        num_dir_l += 1
+
+                max_paralogs = max(max_paralog_list) if max(max_paralog_list) > max_paralogs else max_paralogs
+
+                node['layer'] = {
+                    'Paralogs': max(max_paralog_list) - 1,
+                    'Direction': 1 - max(num_dir_r, num_dir_l)/num,
+                    'Functional_Homogeneity': 1 - max(func_homogeneity_list),
+                    'Geometric_Homogeneity': 1 - max(geo_homogeneity_list),
+                    'Combined_Homogeneity': 1 - max(comb_homogeneity_list)
+                }
+
+        self.data_table_dict['Functional_Homogeneity'] = {
+            'max': 1,
+            'min': 0
+        }
+        self.data_table_dict['Geometric_Homogeneity'] = {
+            'max': 1,
+            'min': 0
+        }
+        self.data_table_dict['Combined_Homogeneity'] = {
+            'max': 1,
+            'min': 0
+        }
+        self.data_table_dict['Paralogs'] = {
+            'max': max_paralogs - 1 if max_paralogs - 1 != 0 else 1,
+            'min': 0
+        }
+        self.data_table_dict['Direction'] = {
+            'max': 0.5,
+            'min': 0
+        }
+
+        self.run.info_single("Done")
+
+
+    def get_additional_gene_layer_table(self):
+
+        self.run.warning(None, header="Export empty dataframe for genecall annotations", lc="green")
+
+        gene_layer_dict = {}
+
+        i = 0
+        for node, data in self.ancest.nodes(data=True):
+            if node != 'start' and node != 'stop':
+                for genome in data['genome'].keys():
+                    contig = data['genome'][genome]['contig']
+                    genecall = data['genome'][genome]['gene_call']
+
+                    gene_layer_dict[i] = {'genome': genome, 'contig': contig, 'genecall': genecall, 'value': 0}
+                    i += 1
+
+        gene_layer_df = pd.DataFrame.from_dict(gene_layer_dict, orient='index')
+
+        gene_layer_df.to_csv(self.output_raw_gene_additional_data, index=False)
+
+        self.run.info_single("Done")
+
+
+    def get_additional_gc_layer_table(self):
+
+        self.run.warning(None, header="Export empty dataframe for gc annotations", lc="green")
+
+        gc_layer_dict = {}
+        included = set()
+
+        i = 0
+        for node, data in self.ancest.nodes(data=True):
+            if node != 'start' and node != 'stop':
+                name = data['name']
+                if name not in included:
+                    gc_layer_dict[i] = {'genecluster': name, 'value': 0}
+                    included.add(name)
+                    i += 1
+
+        gc_layer_df = pd.DataFrame.from_dict(gc_layer_dict, orient='index')
+
+        gc_layer_df.to_csv(self.output_raw_gc_additional_data, index=False)
+
+        self.run.info_single("Done")
+
+
+    def add_additional_gene_layer_values(self):
+
+        self.run.warning(None, header="Appending layer values from external gene data", lc="green")
+
+        df = pd.read_csv(self.gene_additional_data)
+        df.set_index(['genome', 'contig', 'genecall'], inplace=True)
+        layer_names = list(df.columns)
+        layer_max = {layer_name: 0 for layer_name in layer_names}
+
+        for node, data in self.ancest.nodes(data=True):
+
+            if node != 'start' and node != 'stop':
+
+                for layer_name in layer_names:
+                    value_list = []
+
+                    for genome in data['genome'].keys():
+
+                        contig = data['genome'][genome]['contig']
+                        genecall = data['genome'][genome]['gene_call']
+
+                        value = df.loc[(genome, contig, genecall)][layer_name].item()
+                        value_list.append(value)
+
+                    value_sum = sum(value_list) / len(value_list)
+
+                    data['layer'][layer_name] = value_sum
+                    layer_max[layer_name] = layer_max[layer_name] if layer_max[layer_name] > value_sum else value_sum
+
+        for layer_name in layer_names:
+
+            self.data_table_dict[layer_name] = {
+                'max': layer_max[layer_name],
+                'min': 0
+            }
+
+        self.run.info_single("Done")
+
+
+    def add_additional_gc_layer_values(self):
+
+        self.run.warning(None, header="Appending layer values from external gc data", lc="green")
+
+        df = pd.read_csv(self.gc_additional_data)
+        df.set_index(['genecluster'], inplace=True)
+        layer_names = list(df.columns)
+        layer_max = {layer_name: 0 for layer_name in layer_names}
+
+        for node, data in self.ancest.nodes(data=True):
+            if node != 'start' and node != 'stop':
+                name = data['name']
+                for layer_name in layer_names:
+
+                    value = df.loc[name][layer_name].item()
+                    data['layer'][layer_name] = value
+                    layer_max[layer_name] = layer_max[layer_name] if layer_max[layer_name] > value else value
+
+        for layer_name in layer_names:
+
+            self.data_table_dict[layer_name] = {
+                'max': layer_max[layer_name],
+                'min': 0
+            }
+
+        self.run.info_single("Done")
+
+
+    def walk_one_step(self, G, current, nodes_position_dict, visited):
+        successors = [successor for successor in G.successors(current) if successor not in visited]
+        predecessors = [predecessor for predecessor in G.predecessors(current) if predecessor not in visited]
+
+        current_position_x, current_position_y = nodes_position_dict[current]
+        
+        if len(successors) > 0:
+            
+            nodes_position = [(nodes_position_dict[successor][0] - current_position_x, successor) for successor in successors]
+            successor_position, successor = sorted(nodes_position)[0]
+            
+            successor_position_x, successor_position_y = nodes_position_dict[successor]        
+            return(successor_position_x, successor_position_y, successor)
+
+        elif len(predecessors) > 0:
+            nodes_position = [(current_position_x - nodes_position_dict[predecessor][0], predecessor) for predecessor in predecessors]
+            predecessor_position, predecessor = sorted(nodes_position, reverse=True)[0]
+            
+            predecessor_position_x, predecessor_position_y = nodes_position_dict[predecessor]
+            return(predecessor_position_x, predecessor_position_y, predecessor)
+
+        else:
+            return(-1, -1, '')
+
+
+    def is_node_core(self, node):
+        if set(self.ancest.nodes()[node]['genome'].keys()) == set(self.genomes_names):
+            return(True)
+        else:
+            return(False)
+
+
+    def get_genomic_motifs(self):
+
+        self.run.warning(None, header="Generate pangenome graph summary tables", lc="green")
+
+        graph_min = self.ancest.nodes()['start']['pos'][0] + 1
+        graph_max = self.ancest.nodes()['stop']['pos'][0] - 1
+
+        region_id = 0
+        regions = {}
+        region_sides = {}
+
+        for genome in self.genomes_names:
+            # print(genome)
+
+            G_subset_nodes = [n for n,d in self.ancest.nodes(data='genome') if genome not in d.keys()]
+            G_subset_edges = [(i,j) for i,j,d in self.ancest.edges(data='genome') if genome not in d.keys()]
+            G3 = self.ancest.copy()
+            G3.remove_nodes_from(['start', 'stop'] + G_subset_nodes)
+            G3.remove_edges_from(G_subset_edges)
+
+            region_type = {}
+            regions_reverse = []
+            nodes_position_dict = dict(G3.nodes(data="pos"))
+
+            starting_points = []
+            for node in list(G3.nodes()):
+                if len(list(G3.successors(node))) <= 1 and len(list(G3.predecessors(node))) == 0:
+                    starting_points += [node]
+
+            starting_points = sorted(starting_points, key=lambda x: nodes_position_dict[x][0]) 
+
+            # Prepare first starting point in data structure
+            node = starting_points[0]
+            starting_points.remove(node)
+
+            node_position_x, node_position_y = nodes_position_dict[node]
+            former_position = node_position_x
+
+            region_id += 1
+
+            # gene cluster core?
+            if self.is_node_core(node):
+                # start new core region
+                regions[region_id] = [(node_position_x, node_position_y, node)]
+                is_core = True
+            else:
+                # start new accessory region
+                regions[region_id] = [(node_position_x, node_position_y, node)]
+                is_core = False
+
+            visited = set([node])
+            mode = ''
+
+            while True:
+                node_position_x, node_position_y, node = self.walk_one_step(G3, node, nodes_position_dict, visited)
+
+                if node:
+                    mode = ''
+                else:
+                    if starting_points:
+                        node = starting_points[0]
+                        starting_points.remove(node)
+                        node_position_x, node_position_y = nodes_position_dict[node]
+                        direction = ''
+                        mode = 'break'
+                    else:
+                        break
+                
+                # extend current region?
+                if node_position_x == former_position + 1 or node_position_x == (former_position - graph_max) + 1:
+                    # extend core region?
+                    if is_core:
+                        # gene cluster core?
+                        if self.is_node_core(node):
+                            # extend core region with core gene cluster
+                            regions[region_id] += [(node_position_x, node_position_y, node)]
+                            is_core = True
+                        else:
+                            # end core region
+                            region_type[region_id] = ('core', regions[region_id][0][0], regions[region_id][-1][0])
+                            region_id += 1
+
+                            # start accessory region
+                            regions[region_id] = [(node_position_x, node_position_y, node)]
+                            is_core = False
+                    else:
+                        # gene cluster core?
+                        if self.is_node_core(node):
+                            # end accessory region
+                            region_type[region_id] = ('accessory', regions[region_id][0][0], regions[region_id][-1][0])
+                            region_id += 1
+
+                            # start core region
+                            regions[region_id] = [(node_position_x, node_position_y, node)]
+                            is_core = True
+                        else:
+                            # extend accessory region
+                            regions[region_id] += [(node_position_x, node_position_y, node)]
+                            is_core = False
+
+                elif node_position_x == former_position:
+                    if is_core:
+                        region_type[region_id] = ('core', regions[region_id][0][0], regions[region_id][-1][0])
+                    else:
+                        region_type[region_id] = ('accessory', regions[region_id][0][0], regions[region_id][-1][0])
+
+                    region_id += 1
+
+                    if self.is_node_core(node):
+                        # start new core region
+                        regions[region_id] = [(node_position_x, node_position_y, node)]
+                        is_core = True
+                    else:
+                        # start new accessory region
+                        regions[region_id] = [(node_position_x, node_position_y, node)]
+                        is_core = False
+
+                # new forward bridge region? 
+                elif (node_position_x > former_position + 1 and abs(node_position_x - former_position) <= graph_max / 2) or (node_position_x < former_position + 1 and abs(former_position - node_position_x) > graph_max / 2):
+                    # is the region to end core?
+                    if is_core:  
+                        region_type[region_id] = ('core', regions[region_id][0][0], regions[region_id][-1][0])
+                    else:
+                        region_type[region_id] = ('accessory', regions[region_id][0][0], regions[region_id][-1][0])
+
+                    region_id += 1
+
+                    if node_position_x > former_position + 1:
+                        regions[region_id] = [(i, '', '') for i in range(former_position + 1, node_position_x, 1)]
+                    else:
+                        regions[region_id] = [(i, '', '') for i in range(former_position + 1, graph_max + 1, 1)] + [(i, '', '') for i in range(graph_min, node_position_x, 1)]
+
+                    if mode == 'break':
+                        region_type[region_id] = ('break', regions[region_id][0][0], regions[region_id][-1][0])
+                    else:
+                        region_type[region_id] = ('forward', regions[region_id][0][0], regions[region_id][-1][0])
+
+                    region_id += 1
+
+                    # gene cluster core?
+                    if self.is_node_core(node):
+                        # start new core region
+                        regions[region_id] = [(node_position_x, node_position_y, node)]
+                        is_core = True
+                    else:
+                        # start new accessory region
+                        regions[region_id] = [(node_position_x, node_position_y, node)]
+                        is_core = False
+
+                # new backward bridge region?
+                elif (node_position_x < former_position + 1 and abs(former_position - node_position_x) <= graph_max / 2) or (node_position_x > former_position + 1 and abs(node_position_x - former_position) > graph_max / 2):
+                    # is the region to end core?
+                    if is_core:  
+                        region_type[region_id] = ('core', regions[region_id][0][0], regions[region_id][-1][0])
+                    else:
+                        region_type[region_id] = ('accessory', regions[region_id][0][0], regions[region_id][-1][0])
+
+                    region_id += 1
+
+                    if node_position_x < former_position + 1:
+                        regions[region_id] = [(i, '', '') for i in range(former_position - 1, node_position_x, -1)]
+                    else:
+                        regions[region_id] = [(i, '', '') for i in range(former_position - 1, graph_min - 1, -1)] + [(i, '', '', '', genome) for i in range(graph_max, node_position_x, -1)]
+
+                    region_type[region_id] = ('reverse', regions[region_id][0][0], regions[region_id][-1][0])
+
+                    # mark a backward bridge region
+                    regions_reverse += [(regions[region_id][0][0], regions[region_id][-1][0])]
+                    region_id += 1
+                    
+                    # gene cluster core?
+                    if self.is_node_core(node):
+                        # start new core region
+                        regions[region_id] = [(node_position_x, node_position_y, node)]
+                        is_core = True
+                    else:
+                        # start new accessory region
+                        regions[region_id] = [(node_position_x, node_position_y, node)]
+                        is_core = False
+
+                else:
+                    print('A motif of this type is not yet implemented as we never saw it before.')
+
+                visited.add(node)
+                former_position = node_position_x
+
+            if is_core:  
+                region_type[region_id] = ('core', regions[region_id][0][0], regions[region_id][-1][0])
+            else:
+                region_type[region_id] = ('accessory', regions[region_id][0][0], regions[region_id][-1][0])       
+
+            for region_id_inner, region_tuple in region_type.items():
+                # overlap = False
+                # for region_reverse in regions_reverse:
+
+                #     if region_tuple[1] == region_reverse[0] and region_tuple[2] == region_reverse[1]:
+                #         overlap = True
+                    
+                #     elif region_tuple[1] <= region_tuple[2] and region_reverse[0] >= region_reverse[1]:
+                #         # reverse: 15 -> 12
+                #         # current: 13 -> 16
+                        
+                #         #    ------------
+                #         # ------------
+                #         # 12 13 14 15 16
+            
+                #         # left_difference: abs(12 - 13) = 1
+                #         # right_difference: abs(15 - 16) = 1
+                #         # region_compare_size: (16 - 12) + 1 = 5
+                #         # region_overlap_size = 5 - (1 +  1) = 3
+            
+                #         # region_reverse_size: (15 - 12) + 1 = 4
+                #         # region_current_size: (16 - 13) + 1 = 4
+            
+                #         # test: 3 >= (4 * (1/2)) = True
+            
+                #         left_difference = abs(min(region_tuple[1], region_tuple[2]) - min(region_reverse[0], region_reverse[1]))
+                #         right_difference = abs(max(region_tuple[1], region_tuple[2]) - max(region_reverse[0], region_reverse[1]))
+                #         region_compare_size = (max(region_tuple[1], region_tuple[2], region_reverse[0], region_reverse[1]) - min(region_tuple[1], region_tuple[2], region_reverse[0], region_reverse[1])) + 1
+                #         region_overlap_size = region_compare_size - (left_difference +  right_difference)
+            
+                #         region_reverse_size = (max(region_reverse[0], region_reverse[1]) - min(region_reverse[0], region_reverse[1])) + 1
+                #         region_current_size = (max(region_tuple[1], region_tuple[2]) - min(region_tuple[1], region_tuple[2])) + 1
+            
+                #         if region_overlap_size >= (region_current_size / 2):
+                #             overlap = True
+
+                #     else:
+                #         print('A rearrangement event over the start and end border of the graph is not yet implemented')
+                
+                # if overlap:
+                #     region_sides[region_id_inner] = {'start': region_tuple[1], 'end': region_tuple[2], 'types': region_tuple[0], 'consensus': 1.0, 'motif': 'reassortment'}
+                # else:
+                region_sides[region_id_inner] = {'start': region_tuple[1], 'end': region_tuple[2], 'types': region_tuple[0], 'genome': genome, 'consensus': -1, 'motif': ''}
+        
+        tab = pd.DataFrame.from_dict(region_sides, orient='index')
+        tab.rename_axis("region_id", inplace=True)
+        tab.sort_values(['start', 'end'], inplace=True)
+        
+        drop_rows = []
+        groups = tab.groupby(['genome', 'types'])
+        # come up with grouping like 0-10, 0-6, 7-10 end up in one group 
+        # easy search for all connections from i = 0 -> 5, 8, 10 take the highest
+        # i = 0 ... 10 then pick all fragments inside of 0 and 10 e.g. 0 ... 5, 4 ... 8
+        # then check every position for at most every genome once before combine
+        for name, group in groups:
+
+            i = 0
+            j = i + 1
+            while i < len(group) - 1:
+
+                row_i = group.iloc[i]
+                start_i, end_i, types_i, genome_i, consensus_i, motif_i = row_i
+                index_i = row_i.name
+        
+                row_j = group.iloc[j]
+                start_j, end_j, types_j, genome_j, consensus_j, motif_j = row_j
+                index_j = row_j.name
+                
+                if (end_i + 1) == start_j:
+                    end_new = max(end_i, end_j)
+
+                    tab.at[index_i, 'end'] = end_new
+                    drop_rows += [index_j]
+                    
+                    regions[index_i] += regions[index_j]
+                    regions.pop(index_j)
+                    tab.drop(index=index_j, inplace=True)
+
+                    j += 1
+
+                else:
+                    i = j + 1
+                    j = i + 1
+
+        # return(regions, all_nodes)
+        tab.reset_index(drop=False, inplace=True)
+        tab['motif_id'] = tab.loc[:, 'region_id']
+
+        # for key in regions.keys():
+        #     regions[key] = set(regions[key])
+        
+        groups = tab.groupby(['start', 'end'])
+        for name, group in groups:
+        
+            types_list = list(group['types'])
+        
+            if len(set(types_list)) == 1 and len(types_list) <= len(self.genomes_names):
+        
+                joining_list = sorted([(i, j, True) if regions[group.at[i,'motif_id']] == regions[group.at[i,'motif_id']] else (i, j, False) for i, j in it.combinations(group.index, 2)])
+                
+                for index_i, index_j, join_boolean in joining_list:
+                    if join_boolean:
+                        region_id_i, start_i, end_i, types_i, consensus_i, genome_i, motif_i, motif_id_i = tab.loc[index_i]
+                        region_id_j, start_j, end_j, types_j, consensus_j, genome_j, motif_j, motif_id_j = tab.loc[index_j]
+                    
+                        tab.at[index_j, 'motif_id'] = motif_id_i
+                        tab.at[index_j, 'motif_id'] = motif_id_i
+
+                        tab.at[index_i, 'consensus'] = 1.0
+                        tab.at[index_j, 'consensus'] = 1.0
+                        
+                        tab.at[index_i, 'motif'] = 'hypervariability' if types_i == 'accessory' and len(types_list) == len(self.genomes_names) else types_i
+                        tab.at[index_j, 'motif'] = 'hypervariability' if types_i == 'accessory' and len(types_list) == len(self.genomes_names) else types_i
+
+                        # regions[region_id_i] += regions[region_id_j]
+                        
+            elif set(types_list) == set(['forward', 'accessory']) and len(types_list) <= len(self.genomes_names):
+        
+                forward_group = group[group["types"] == 'forward']
+                accessory_group = group[group["types"] == 'accessory']
+                
+                joining_equal = all([True if regions[accessory_group.at[i,'motif_id']] == regions[accessory_group.at[i,'motif_id']] else False for i, j in it.combinations(accessory_group.index, 2)])
+                joining_list = sorted([(i, j, True) if regions[group.at[i,'motif_id']] == regions[group.at[i,'motif_id']] else (i, j, False) for i, j in it.combinations(group.index, 2)])
+                
+                for index_i, index_j, join_boolean in joining_list:
+                    if join_boolean:
+                        region_id_i, start_i, end_i, types_i, consensus_i, genome_i, motif_i, motif_id_i = tab.loc[index_i]
+                        region_id_j, start_j, end_j, types_j, consensus_j, genome_j, motif_j, motif_id_j = tab.loc[index_j]
+                        
+                        tab.at[index_j, 'motif_id'] = motif_id_i
+                        tab.at[index_j, 'motif_id'] = motif_id_i
+
+                        if joining_equal:
+                            a = len(forward_group)
+                            b = len(accessory_group)
+                            if a >= b:
+                                consensus = round(a / (a+b), 3)
+                                motif = 'insertion'
+                            else:
+                                consensus = round(b / (a+b), 3)
+                                motif = 'deletion'
+                        else:
+                            consensus = 1.0
+                            motif = 'hypervariability'
+
+                        tab.at[index_i, 'consensus'] = consensus
+                        tab.at[index_j, 'consensus'] = consensus
+
+                        tab.at[index_i, 'motif'] = motif
+                        tab.at[index_j, 'motif'] = motif
+
+                        # regions[region_id_i] += regions[region_id_j]
+                
+            elif set(types_list) == set(['break', 'accessory']) and len(types_list) <= len(self.genomes_names):
+                
+                joining_equal = all([True if regions[accessory_group.at[i,'motif_id']] == regions[accessory_group.at[i,'motif_id']] else False for i, j in it.combinations(accessory_group.index, 2)])
+                joining_list = sorted([(i, j, True) if regions[group.at[i,'motif_id']] == regions[group.at[i,'motif_id']] else (i, j, False) for i, j in it.combinations(group.index, 2)])
+                
+                for index_i, index_j, join_boolean in joining_list:
+                    if join_boolean:
+                        region_id_i, start_i, end_i, types_i, consensus_i, genome_i, motif_i, motif_id_i = tab.loc[index_i]
+                        region_id_j, start_j, end_j, types_j, consensus_j, genome_j, motif_j, motif_id_j = tab.loc[index_j]
+                    
+                        tab.at[index_j, 'motif_id'] = motif_id_i
+                        tab.at[index_j, 'motif_id'] = motif_id_i
+
+                        if joining_equal:
+                            consensus = 1.0
+                            motif = 'broken core'
+                        else:
+                            consensus = 1.0
+                            motif = 'hypervariability'
+
+                        tab.at[index_i, 'consensus'] = consensus
+                        tab.at[index_j, 'consensus'] = consensus
+
+                        tab.at[index_i, 'motif'] = motif
+                        tab.at[index_j, 'motif'] = motif
+
+                        # regions[region_id_i] += regions[region_id_j]
+
+            else:
+                continue
+
+        tab.sort_values(['start', 'end'], inplace=True)
+        tab.reset_index(drop=True, inplace=True)
+
+        groups = tab.groupby(['motif_id'])
+        nodes_dict_id = 0
+        nodes_dict = {}
+        for motif_id, group in groups:
+
+            for index, row in group.iterrows():
+
+                region_id = row['region_id']
+                genome = row['genome']
+
+                for region in regions[region_id]:
+                    node_position_x, node_position_y, node = region
+
+                    if node:
+                        nodes_dict[nodes_dict_id] = {'motif_id': motif_id, 'node_position_x': node_position_x, 'node_position_y': node_position_y, 'gene_cluster_id': node, 'genome': genome}
+                        nodes_dict_id += 1
+
+        tab2 = pd.DataFrame.from_dict(nodes_dict, orient='index').set_index(['gene_cluster_id', 'genome'])
+        tab1 = tab.drop(['region_id'], axis=1).set_index(['motif_id', 'genome'])
+        
+        nodes_dict = {n:d for n,d in self.ancest.nodes(data='genome')}
+        tab3 = pd.DataFrame.from_dict(
+            {(i,j): nodes_dict[i][j]
+            for i in nodes_dict.keys()
+            for j in nodes_dict[i].keys()
+            if i != 'start' and i != 'stop'}, orient='index')
+        
+        tab3.drop('gene_cluster_id', inplace=True, axis=1)
+        tab3.rename_axis(['gene_cluster_id', 'genome'], inplace=True)
+
+        for source in self.functional_annotation_sources_available:
+            tab3[source] = tab3[source].apply(lambda x: ('None', 'None', 'None') if x == 'None' else x)
+            tab3[[source + '_ID', source + 'TEXT', source + '_E_VALUE']] = pd.DataFrame(tab3[source].values.tolist(), index=tab3.index)
+            tab3.drop(source, inplace=True, axis=1)
+
+        tab3.fillna('None', inplace=True)
+        tab4 = pd.merge(tab2, tab3, how='left', on=['gene_cluster_id', 'genome'])
+        
+        if len(tab2) != len(tab3):
+            self.run.info_single('Genecall entries are missing from the result table!')
+            
+        tab1.to_csv(self.output_summary + '/motifs.tsv', sep='\t')
+        tab4.to_csv(self.output_summary + '/genes.tsv', sep='\t')
+
+        self.run.info_single("Done")
+
+
+    def update_json_dict(self):
+        self.run.warning(None, header="Update JSON dictionary for export", lc="green")
+
+        self.jsondata["infos"]['meta']['global_y'] = self.global_y
+        self.jsondata["infos"]['meta']['global_x_offset'] = self.global_x_offset
+        self.jsondata["infos"]['max_edge_length_filter'] = self.max_edge_length_filter
+        self.jsondata["infos"]['gene_cluster_grouping_threshold'] = self.gene_cluster_grouping_threshold
+        self.jsondata["infos"]['groupcompress'] = self.groupcompress
+        self.jsondata["infos"]['ungroup'] = self.ungroup
+        self.jsondata["infos"]['layout_graph']['edges'] = len(self.ancest.edges())
+        self.jsondata["infos"]['data'] = list(self.ancest.graph.items())
+        self.jsondata["infos"]['directed'] = self.ancest.is_directed()
+        self.jsondata["infos"]['groups'] = self.grouping
+        self.jsondata['infos']['grouped'] = {'nodes': len(self.ancest.nodes()), 'edges': len(self.ancest.edges())}
+
+        for i, j in self.ancest.nodes(data=True):
+            self.jsondata["elements"]["nodes"][str(i)]["position"]['y'] = j['pos'][1]
+            self.jsondata["elements"]["nodes"][str(i)]["position"]['x_offset'] = self.offset[i]
+
+        for edge in self.jsondata["elements"]["edges"]:
+            source = self.jsondata["elements"]["edges"][edge]["source"]
+            target = self.jsondata["elements"]["edges"][edge]["target"]
+            self.jsondata["elements"]["edges"][edge]["shown"] = 1
+
+            if (source, target) in self.removed:
+                self.jsondata["elements"]["edges"][edge]["shown"] = 0
+                self.jsondata["elements"]["edges"][edge]["bended"] = ""
+
+            elif self.ancest.has_edge(source, target):
+                self.jsondata["elements"]["edges"][edge]["bended"] = [{'x': x, 'y': y} for x, y in self.ancest[source][target]["bended"]] if len(self.ancest[source][target]["bended"]) != 0 else ""
+
+        self.run.info_single("Done")
+
+
+    # TODO rework that section for better debugging and add more features as an example fuse start and top
+    # together or remove both so the graph becomes a REAL circle. Aside from that there is a bug in the remove
+    # edges section for (k,o) in circular edges and for (k,o) in pangenome edges. Change and test while reworking.
+    def get_json_dict_for_graph(self):
+        self.run.warning(None, header="Calculating syntenous distances", lc="green")
+
+        # NOTE: Any change in `self.jsondata` will require the pangraph JSON in anvio.tables.__init__
+        #       to incrase by one (so that the new code that works with the new structure requires
+        #       previously generated JSON to be recomputed).
+
+        nodes_all = len(self.ancest.nodes())
+        edges_all = len(self.ancest.edges())
+
+        X = np.zeros([len(self.genomes_names), len(self.genomes_names)])
+        for genome_i, genome_j in it.combinations(self.genomes_names, 2):
+            nodes_similar = 0
+            edges_similar = 0
+            nodes_unsimilar = 0
+            edges_unsimilar = 0
+            for _, data in self.ancest.nodes(data=True):
+                if genome_i in data['genome'].keys() and genome_j in data['genome'].keys():
+                    nodes_similar += 1
+                elif genome_i in data['genome'].keys() or genome_j in data['genome'].keys():
+                    nodes_unsimilar += 1
+            for _, _, data in self.ancest.edges(data=True):
+                if genome_i in data['genome'].keys() and genome_j in data['genome'].keys():
+                    edges_similar += 1
+                elif genome_i in data['genome'].keys() or genome_j in data['genome'].keys():
+                    edges_unsimilar += 1
+
+            i = self.genomes_names.index(genome_i)
+            j = self.genomes_names.index(genome_j)
+
+            elements_similar = nodes_similar + edges_similar
+            elements_unsimilar = nodes_unsimilar + edges_unsimilar
+            elements_all = nodes_all + edges_all
+
+            X[i][j] = elements_unsimilar / (elements_similar + elements_unsimilar)
+            X[j][i] = elements_unsimilar / (elements_similar + elements_unsimilar)
+
+            self.run.info_single(f"{genome_i} and {genome_j}: {round(X[i][j], 3)}")
+
+        condensed_X = squareform(X)
+        Z = linkage(condensed_X, 'ward')
+        tree = to_tree(Z, False)
+        newick = clustering.get_newick(tree, tree.dist, self.genomes_names)
+
+        if self.output_graphics:
+            fig = plt.figure(figsize=(25, 10))
+            ax = plt.axes()
+            dn = dendrogram(Z, ax=ax, labels=self.genomes_names, orientation='right')
+            plt.tight_layout()
+            fig.savefig(self.output_graphics + 'phylogenie' + '.pdf')
+
+        self.run.info_single("Done.")
+        self.run.warning(None, header="Creating JSON dictionary for export", lc="green")
+
+        self.jsondata["infos"] = {
+            'meta': {
+                'title': self.project_name,
+                'version': anvio.__pangraph__version__,
+                'global_x': self.global_x,
+                'global_y': self.global_y,
+                'global_x_offset': self.global_x_offset
+            },
+            'genomes': {genome: 'on' for genome in self.genomes},
+            'functional_annotation_sources_available': self.functional_annotation_sources_available,
+            'num_genomes': len(self.genomes),
+            'max_edge_length_filter': self.max_edge_length_filter,
+            'gene_cluster_grouping_threshold': self.gene_cluster_grouping_threshold,
+            'groupcompress': self.groupcompress,
+            'ungroup': self.ungroup,
+            'priority_genome': self.priority_genome,
+            'newick': newick,
+            'layout_graph': {
+                'nodes': len(self.ancest.nodes()),
+                'edges': len(self.ancest.edges())
+            },
+            'data': list(self.ancest.graph.items()),
+            'directed': self.ancest.is_directed(),
+            'groups': self.grouping,
+            'grouped': {
+                'nodes': len(self.ancest.nodes()),
+                'edges': len(self.ancest.edges())
+            },
+            'layers_data': self.data_table_dict
+        }
+
+        self.jsondata['elements'] = {
+            'nodes': {},
+            'edges': {}
+        }
+
+        for i, j in self.ancest.nodes(data=True):
+
+            self.jsondata["elements"]["nodes"][str(i)] = {
+                "name": j["name"],
+                "weight": j["weight"],
+                "layer": j["layer"],
+                "position": {
+                    'x': j['pos'][0],
+                    'y': j['pos'][1],
+                    'x_offset': self.offset[i]
+                },
+                "genome": {key: {item: j["genome"][key][item] for item in ['gene_call', 'contig', 'direction']} for key in j["genome"].keys()}
+            }
+
+        for l, (k, o, m) in enumerate(self.ancest.edges(data=True)):
+
+            self.jsondata["elements"]["edges"]['E_' + str(l).zfill(8)] = {
+                "source": k,
+                "target": o,
+                "shown": 1,
+                "genome": m["genome"],
+                "weight": m["weight"],
+                "direction": m["direction"],
+                "bended": [{'x': x, 'y': y} for x, y in m["bended"]] if len(m["bended"]) != 0 else ""
+            }
+
+        self.run.info_single("Done.")
+
+
+    def store_network(self):
+        """Function to store final graph structure in a pan-db and/or JSON flat text output file"""
+
+        self.run.warning(None, header="Exporting pangenome graph to JSON", lc="green")
+
+        if self.output_graphml:
+
+            graphml = nx.DiGraph()
+            graphml.add_nodes_from([n for n, d in self.ancest.nodes(data=True)])
+            graphml.add_edges_from([(i, j) for i, j, d in self.ancest.edges(data=True)])
+
+            nx.write_graphml_lxml(graphml, self.output_graphml)
+            self.run.info("GraphML output file", os.path.abspath(self.output_graphml))
+
+        if self.json_output_file_path:
+
+            filesnpaths.is_output_file_writable(self.json_output_file_path)
+
+            with open(self.json_output_file_path, 'w') as output:
+                output.write(json.dumps(self.jsondata, indent=2))
+            self.run.info("JSON output file", os.path.abspath(self.json_output_file_path))
+        else:
+            self.run.info("JSON output file", "Skipped (but OK)", mc='red')
+
+        if not self.skip_storing_in_pan_db:
+            raise ConfigError("The storage of graph data in pan-db is not yet implemented :/")
+        else:
+            self.run.info("Into the pan-db", "Skipped (but OK)", mc='red')
+
+        self.run.info_single("Done")
\ No newline at end of file
diff --git a/anvio/tables/__init__.py b/anvio/tables/__init__.py
index 6ef632fe1..5b1a71601 100644
--- a/anvio/tables/__init__.py
+++ b/anvio/tables/__init__.py
@@ -24,6 +24,9 @@
 workflow_config_version = "3"
 metabolic_modules_db_version = "4"
 
+# versions of key text data types
+pangraph_json_version = "2"
+
 versions_for_db_types = {'contigs': contigs_db_version,
                          'profile': profile_db_version,
                          'genes': genes_db_version,
diff --git a/anvio/utils.py b/anvio/utils.py
index 6aa091f54..684408bb2 100644
--- a/anvio/utils.py
+++ b/anvio/utils.py
@@ -4439,6 +4439,21 @@ def get_yaml_as_dict(file_path):
                           f"{file_path} as a YAML file. It is likely that it is not a properly "
                           f"formatted YAML file and it needs editing, but here is the error "
                           f"message in case it clarifies things: '{e}'.")
+    
+def save_dict_as_yaml(data, file_path):
+    """YAML parser"""
+
+    filesnpaths.is_output_file_writable(file_path)
+
+    try:
+        with open(file_path, 'w') as outfile:
+            yaml.dump(data, outfile, default_flow_style=False)
+
+    except Exception as e:
+        raise ConfigError(f"Anvi'o run into some trouble when trying to parse the file at "
+                          f"{file_path} as a YAML file. It is likely that it is not a properly "
+                          f"formatted YAML file and it needs editing, but here is the error "
+                          f"message in case it clarifies things: '{e}'.")
 
 
 def download_file(url, output_file_path, check_certificate=True, progress=progress, run=run):
diff --git a/bin/anvi-display-pan-graph b/bin/anvi-display-pan-graph
new file mode 100755
index 000000000..e3cbb7da8
--- /dev/null
+++ b/bin/anvi-display-pan-graph
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+# -*- coding: utf-8
+
+import sys
+from anvio.argparse import ArgumentParser
+
+import anvio
+import anvio.utils as utils
+import anvio.terminal as terminal
+import anvio.interactive as interactive
+from anvio.bottleroutes import BottleApplication
+
+from anvio.errors import ConfigError, FilesNPathsError, DictIOError
+
+__author__ = "Developers of anvi'o (see AUTHORS.txt)"
+__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
+__credits__ = []
+__license__ = "GPL 3.0"
+__version__ = anvio.__version__
+__authors__ = ['ahenoch']
+__requires__ = ['pan-graph-json']
+__provides__ = ['interactive', 'svg']
+__description__ = "Start an anvi'o interactive interface to view pan graphs."
+
+run = terminal.Run()
+progress = terminal.Progress()
+
+if __name__ == '__main__':
+    parser = ArgumentParser(description=__description__)
+    groupA = parser.add_argument_group('PRIMARY INPUT', "Specify where your pan-db is.")
+    groupA.add_argument(*anvio.A('pan-db'), **anvio.K('pan-db', {'required': False}))
+    groupA.add_argument(*anvio.A('genomes-storage'), **anvio.K('genomes-storage', {'required': False}))
+
+    groupB = parser.add_argument_group('OPTIONAL INPUT', "By default, this program will read the pan graph data from the pan-db tables. However, "
+                                "you can also provide it with a JSON file that you have generated previously, in which case the program will skip "
+                                "attempting to read anything from the pan-db and will use the input file to initialize an interface.")
+    groupB.add_argument(*anvio.A('pan-graph-json'), **anvio.K('pan-graph-json'))
+    
+    groupC = parser.add_argument_group('SERVER CONFIGURATION', "For power users.")
+    groupC.add_argument(*anvio.A('dry-run'), **anvio.K('dry-run'))
+    groupC.add_argument(*anvio.A('ip-address'), **anvio.K('ip-address'))
+    groupC.add_argument(*anvio.A('port-number'), **anvio.K('port-number'))
+    groupC.add_argument(*anvio.A('browser-path'), **anvio.K('browser-path'))
+    groupC.add_argument(*anvio.A('server-only'), **anvio.K('server-only'))
+    groupC.add_argument(*anvio.A('password-protected'), **anvio.K('password-protected'))
+
+    args = parser.get_args(parser)
+
+    try:
+        d = interactive.PangraphInteractive(args, run=run, progress=progress)
+
+        if args.dry_run:
+            run.info_single('Dry run, eh? Fine. Bai!', nl_after=1)
+            sys.exit()
+
+        args.mode = 'pangraph'
+        port_number = utils.get_port_num(args.port_number, args.ip_address, run=run)
+
+        app = BottleApplication(d)
+        app.run_application(args.ip_address, port_number)
+    except ConfigError as e:
+        print(e)
+        sys.exit(-1)
+    except FilesNPathsError as e:
+        print(e)
+        sys.exit(-2)
+    except DictIOError as e:
+        print(e)
+        sys.exit(-3)
diff --git a/bin/anvi-pan-graph b/bin/anvi-pan-graph
new file mode 100755
index 000000000..c59ab92b4
--- /dev/null
+++ b/bin/anvi-pan-graph
@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+# -*- coding: utf-8
+"""Compute a graph representation of a pangenome"""
+
+import sys
+
+import anvio
+import anvio.panops as panops
+import anvio.terminal as terminal
+
+from anvio.errors import ConfigError, FilesNPathsError
+
+
+__author__ = "Developers of anvi'o (see AUTHORS.txt)"
+__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
+__credits__ = []
+__license__ = "GPL 3.0"
+__version__ = anvio.__version__
+__authors__ = ['ahenoch']
+__requires__ = ['pan-db', 'genomes-storage-db', 'external-genomes']
+__provides__ = ['pan-graph-json']
+__description__ = ("An anvi'o program to compute a graph representation of pangenomes. It will do its magic, and store it into your "
+                   "pan-db, or report a JSON formatted graph file, for downstream visualization and analyses with `anvi-display-pan-graph`")
+__resources__ = []
+
+
+run = terminal.Run()
+progress = terminal.Progress()
+
+
+if __name__ == '__main__':
+    from anvio.argparse import ArgumentParser
+
+    parser = ArgumentParser(description=__description__)
+
+    groupA = parser.add_argument_group('INPUT', "Anvi'o artifacts for the pan graph to be computed.")
+    groupA.add_argument(*anvio.A('pan-db'), **anvio.K('pan-db', {'required': False}))
+    groupA.add_argument(*anvio.A('genomes-storage'), **anvio.K('genomes-storage', {'required': False}))
+    groupA.add_argument(*anvio.A('external-genomes'), **anvio.K('external-genomes', {'required': False}))
+    groupA.add_argument(*anvio.A('testing-yaml'), **anvio.K('testing-yaml'))
+    groupA.add_argument(*anvio.A('gene-additional-data'), **anvio.K('gene-additional-data'))
+    groupA.add_argument(*anvio.A('gc-additional-data'), **anvio.K('gc-additional-data'))
+    groupA.add_argument(*anvio.A('pan-graph-json'), **anvio.K('pan-graph-json'))
+    groupA.add_argument(*anvio.A('genomes-names'), **anvio.K('genomes-names'))
+    groupA.add_argument(*anvio.A('genomes-reverse'), **anvio.K('genomes-reverse'))
+
+    groupB = parser.add_argument_group('OUTPUT', "By default, this program will store the resulting pangraph into the anvi'o pan-db "
+                                "you have provided as input above, so it is accessible to downstream analyses seamlessly. Using the "
+                                "the parameters below, you can ask anvi'o to store the resulting graph into a text output file (which "
+                                "may be useful for developers for debugging purposes) or you can ask anvi'o to skip adding the results "
+                                "to the pan-db.")
+    groupB.add_argument(*anvio.A('output-graphml'), **anvio.K('output-graphml'))
+    groupB.add_argument(*anvio.A('output-pan-graph-json'), **anvio.K('output-pan-graph-json'))
+    groupB.add_argument(*anvio.A('output-testing-yaml'), **anvio.K('output-testing-yaml'))
+    groupB.add_argument(*anvio.A('output-dir-summary'), **anvio.K('output-dir-summary'))
+    groupB.add_argument(*anvio.A('output-dir-graphics'), **anvio.K('output-dir-graphics'))
+    groupB.add_argument(*anvio.A('output-raw-gene-additional-data'), **anvio.K('output-raw-gene-additional-data'))
+    groupB.add_argument(*anvio.A('output-raw-gc-additional-data'), **anvio.K('output-raw-gc-additional-data'))
+
+    groupB.add_argument('--skip-storing-in-pan-db', default=False, action="store_true", help="Do not store the resulting graph into "
+                                "the pan-db.")
+
+    groupC = parser.add_argument_group('DETAILS OF GRAPH COMPUTATION', "Variables that will influence the computation of the graph, the organization "
+                                "of the gene clusters, and edges between them.")
+    groupC.add_argument('--max-edge-length-filter', default = -1, type=int, help = "In the final pan graph, edges that connect gene clusters will vary in "
+                                "their length. The longer edges that connect far gene clusters with one another will add additional layers to the final "
+                                "display, reducing the readability of the overall graph structure. This parameter, which is by default set to %(default)d, "
+                                "will remove edges that span across more than %(default)d gene clusters. You can change the thresold to make graph much "
+                                "more accurate (lower values) or much more readable (higher values). We suggest you to start with the default, but "
+                                "explore other options if you are not satisfied. Please keep in mind that pangenomes that contain a very large number of "
+                                "genomic rearrangement events may take a very long time to compute with very small values of this parameter.")
+    groupC.add_argument('--gene-cluster-grouping-threshold', default = 2, type=int, help = "This parameters influences how gene clusters that share "
+                                "perfect synteny (across all genomes that contribute genes) are represented in the final display. With the default value "
+                                "of %(default)d, the final graph will represent as many gene clusters as possible in groups.")
+    groupC.add_argument('--gene-cluster-grouping-compression', default = 0.0, type=float, help = "Description.")
+    groupC.add_argument('--ungrouping-area', default = [-1, -1], type=list, help = "Description.")
+    groupC.add_argument('--priority-genome', default = '', type=str, help = "Description.")
+
+    args = parser.get_args(parser)
+
+    try:
+        graph = panops.Pangraph(args, run, progress)
+        graph.process()
+    except ConfigError as e:
+        print(e)
+        sys.exit(-1)
+    except FilesNPathsError as e:
+        print(e)
+        sys.exit(-2)
\ No newline at end of file
diff --git a/bin/anvi-reorient-contigs b/bin/anvi-reorient-contigs
new file mode 100755
index 000000000..6e0043180
--- /dev/null
+++ b/bin/anvi-reorient-contigs
@@ -0,0 +1,177 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+import os
+import sys
+import glob
+import subprocess
+
+from Bio import SeqIO, SearchIO
+from Bio.SeqRecord import SeqRecord
+
+import anvio
+import anvio.fastalib as f
+import anvio.terminal as terminal
+import anvio.filesnpaths as filesnpaths
+
+from anvio.argparse import ArgumentParser
+from anvio.errors import ConfigError, FilesNPathsError
+
+__copyright__ = "Copyleft 2015-2024, The Anvi'o Project (http://anvio.org/)"
+__credits__ = []
+__license__ = "GPL 3.0"
+__version__ = anvio.__version__
+__authors__ = ['ahenoch', 'meren']
+__requires__ = []
+__provides__ = []
+__description__ = "Reorient contigs based on the longest complete genome presend in the given folder"
+
+
+progress = terminal.Progress()
+run = terminal.Run()
+P = terminal.pluralize
+
+
+def get_num_contigs_and_genome_length(file_path):
+    fasta = f.SequenceSource(file_path)
+
+    num_contigs = 0
+    length = 0
+
+    while next(fasta):
+        num_contigs += 1
+        length += len(fasta.seq)
+
+    return(num_contigs, length)
+
+
+def main(args):
+    input_dir = args.input_dir
+    prioritize_genome_size = args.prioritize_genome_size
+    prioritize_number_of_contigs = args.prioritize_number_of_contigs
+
+    reference_fasta = None
+
+    filesnpaths.is_output_dir_writable(input_dir)
+
+    if (not prioritize_genome_size and not prioritize_number_of_contigs) or (prioritize_genome_size and prioritize_number_of_contigs):
+        raise ConfigError("You must choose one of these parameters -- not both, not none: `--prioritize-genome-size` "
+                          "or `--prioritize-number-of-contigs`.")
+
+    # find FASTA files in the user directory and determine the best reference de novo
+    genome_properties = {}
+
+    best_length = 0
+    best_num_contigs = sys.maxsize
+
+    F = lambda x: glob.glob(os.path.join(input_dir, x))
+    input_fasta_files = F('*.fa') + F('*.fasta') + F('*.fna') + F('*.ffn') + F('*.faa')
+
+    run.warning(f"Anvi'o found {P('FASTA file', len(input_fasta_files))} in out input directory, and "
+                f"will try to orient contigs in them based on the best reference in the same directory.",
+                header="FASTA FILES FOUND", lc="yellow")
+
+    for fasta_file in input_fasta_files:
+        num_contigs, length = get_num_contigs_and_genome_length(fasta_file)
+        genome_properties[fasta_file] = {'num_contigs': num_contigs, 'length': length}
+
+        run.info_single(f"{os.path.basename(fasta_file)} ({P('contig', num_contigs)}; {P('nt', length)})", level=2)
+
+        if prioritize_genome_size and length > best_length:
+            reference_fasta = fasta_file
+            best_length = length
+        elif prioritize_number_of_contigs and num_contigs < best_num_contigs:
+            reference_fasta = fasta_file
+            best_num_contigs = num_contigs
+        elif prioritize_number_of_contigs and num_contigs == best_num_contigs:
+            if length > best_length:
+                reference_fasta = fasta_file
+                best_length = length
+        else:
+            # wtf case
+            pass
+
+    run.info("Method to select reference", "Minimum number of contigs" if prioritize_number_of_contigs else "Maximum length", nl_before=1)
+    addtl_info = P('nt', genome_properties[reference_fasta]['length']) if prioritize_genome_size else P('contig', genome_properties[reference_fasta]['num_contigs'])
+    run.info("Reference FASTA", f"{reference_fasta} ({addtl_info})", nl_after=1)
+
+    if genome_properties[reference_fasta]['num_contigs'] != 1:
+        if prioritize_genome_size:
+            raise ConfigError("Sadly, the reference genome anvi'o chose for you based on geonome size priority seems to have multiple contigs, "
+                              "which suggests that it is not a complete genome :/ The current implementation of this script does not know "
+                              "how to use a genome with multiple contigs as reference. You can try to re-run the program with `--prioritize-number-of-contigs` "
+                              "flag if you have a complete genome.")
+        elif prioritize_number_of_contigs:
+            raise ConfigError("The genome in your collection with the smallest number of contigs is still not a complete genome :( There is nothing "
+                              "this program can do for you at this point. Sorry!")
+        else:
+            # wtf case
+            pass
+
+
+    progress.new("BLAST")
+    for fasta_file in input_fasta_files:
+        blast_result_file = '.'.join(fasta_file.split('.')[:-1]) + '-blast.xml'
+
+        if fasta_file != reference_fasta:
+            # run BLAST
+            progress.update(f"Running {os.path.basename(fasta_file)} against the reference ...")
+            cmd_line = ["blastn", "-query", reference_fasta, "-out", blast_result_file, "-outfmt", "5", "-subject", fasta_file]
+            subprocess.run(cmd_line, text=True, capture_output=True)
+
+            progress.update(f"Parsing {os.path.basename(fasta_file)} hits ...")
+            qresult = SearchIO.read(blast_result_file, 'blast-xml')
+            fasta_entry = list(SeqIO.parse(fasta_file, "fasta"))
+
+            with open(fasta_file, "w+") as output_handle:
+                for contig in qresult:
+                    original_record = [entry for entry in fasta_entry if entry.id == contig.id][0]
+
+                    original_record_sequence = original_record.seq
+                    reversed_record_sequence = original_record.seq.reverse_complement()
+
+                    reoriented_record_hit = contig[0].hit.seq.replace("-", "")
+                    reoriented_record_sequence = ""
+
+                    if reoriented_record_hit in original_record_sequence:
+                        reoriented_record_sequence = original_record_sequence
+                    elif reoriented_record_hit in reversed_record_sequence:
+                        reoriented_record_sequence = reversed_record_sequence
+                    else:
+                        pass
+
+                    if reoriented_record_sequence:
+                        reoriented_record = SeqRecord(reoriented_record_sequence, id=original_record.id, name=original_record.name, description=original_record.description)
+                        SeqIO.write(reoriented_record, output_handle, "fasta")
+                    else:
+                        progress.reset()
+                        run.info_single(f"No output possible, the FASTA files do not align :(")
+
+    progress.end()
+
+
+if __name__ == '__main__':
+    parser = ArgumentParser(description=__description__)
+    groupA = parser.add_argument_group('INPUT FILES')
+    groupA.add_argument(*anvio.A('input-dir'), **anvio.K('input-dir', {'help': "Path for the directory "
+                "that contains the FASTA files of interest. Anvi'o will take into consideration any file "
+                "in this directory that has any of the following extensions: '.fa', '.fasta', '.fna', "
+                "'.ffn', and '.faa'."}))
+
+    groupB = parser.add_argument_group('REFERECE GENOME OPTIONS', description="Orienting contigs will require a reference genome that "
+                "must be chosen by none other than YOU.")
+    groupB.add_argument('--prioritize-genome-size', action="store_true", default=False, help="Of all the candidates, choose the genome "
+                        "with largest size as 'reference' to orient contigs in other FASTA files.")
+    groupB.add_argument('--prioritize-number-of-contigs', action="store_true", default=False, help="Of all the candidates, choose the genome "
+                        "with the smallest number of contigs as 'reference' to orient contigs in other FASTA files.")
+
+    args = parser.get_args(parser)
+
+    try:
+        main(args)
+    except ConfigError as e:
+        print(e)
+        sys.exit(-1)
+    except FilesNPathsError as e:
+        print(e)
+        sys.exit(-2)
diff --git a/requirements.txt b/requirements.txt
index c0abfc1d8..5331fdf70 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -22,7 +22,7 @@ pandas==1.4.4
 snakemake
 multiprocess
 plotext
-networkx
+networkx==3.1
 pulp==2.7.0
 biopython
 reportlab
diff --git a/requirements.yml b/requirements.yml
new file mode 100644
index 000000000..612344b67
--- /dev/null
+++ b/requirements.yml
@@ -0,0 +1,65 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconductor-qvalue
+  - biopython
+  - blast
+  - bottle
+  - bowtie2
+  - bwa
+  - colored
+  - diamond
+  - django
+  - ete3
+  - famsa
+  - fastani
+  - fasttree
+  - ghostscript
+  - graphviz
+  - hmmer
+  - idba
+  - illumina-utils
+  - iqtree
+  - matplotlib==3.5.1
+  - mcl
+  - megahit
+  - meme
+  - mistune
+  - multiprocess
+  - muscle=3.8.1551
+  - networkx==3.1
+  - nodejs
+  - numba
+  - numpy[version='<=1.24']
+  - pandas==1.4.4
+  - paste
+  - plotext
+  - prodigal
+  - psutil
+  - pulp==2.7.0
+  - pyani
+  - pymupdf
+  - pysam
+  - python=3.10
+  - r-base
+  - r-magrittr
+  - r-optparse
+  - r-stringi
+  - r-tidyverse
+  - reportlab
+  - requests
+  - rich-argparse
+  - samtools[version='>=1.9']
+  - scikit-learn==1.2.2
+  - scipy
+  - six
+  - snakemake
+  - spades
+  - sqlite
+  - statsmodels
+  - tabulate
+  - trimal
+  - trnascan-se
+  - vmatch