phylopytho

Phylogenetic tools written in python by the Dunn Lab.

Installation

To prepare a conda environment and install phylopytho (before first use):

conda create -n phylopytho -c conda-forge -c bioconda dendropy pytest
conda activate phylopytho
pip install git+https://github.com/dunnlab/phylopytho.git

To activate the conda environment (before each use):

conda activate phylopytho

Conventions

Tip names on trees follow the convention taxon@ID, for example Nematostella_vectensis@301933. taxon can be any name, but is typically Genus_species. ID is a unique identifier. It can be unique to the taxon, or globally unique across all taxa. Avoid spaces or special characters in the names.

treeprune

treeprune, available in the phylopytho module, is a method and tool to decompose gene trees into subtrees that have no more than one tip per species. It does this in two steps - monophyly_prune and paralogy_prune.

paralogy_prune traverses the tree, identifying the maximally inclusive subtree that has no more than one tip per species. It then prunes away and outputs this maximally inclusive subtree. This process is repeated until the remaining tree has no more than one tip per species, at which time the remaining tree is also added to the output. If at any step there are two subtrees with no more than one tip per species and they both have the same size and it is the maximum, they are both pruned. paralogy_prune is not sensitive to the position of the tree root.

Gene trees often have clades of multiple sequences from the same species. These are often technical artifacts, especially in trees based on transcriptome assemblies that can include multiple splice variants per gene which then form monophyletic clades on the gene tree. These monophyletic groups from the same species reduce the size of the maximally inclusive subtrees, and lead paralogy_prune to prune an input tree into a large number of small trees. paralogy_prune can therefore be preceded by monophyly_prune. This method identifies all clades that contain multiple tips exclusively from one species, and randomly masks all but one of those tips.

Please cite the following two papers when publishing analyses that use treeprune. The first manuscript is the original description of the method, the second is the implementation of the method provided in our tool Agalma, from which the stand-alone code provided here is derived.

• Hejnol, A, M Obst, A Stamatakis, M Ott, G Rouse, G Edgecombe, P Martinez, J Baguñà, X Bailly, U Jondelius, M Wiens, WEG Müller, Elaine Seaver, WC Wheeler, MQ Martindale, G Giribet, and CW Dunn (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B. 276:4261-4270 http://dx.doi.org/10.1098/rspb.2009.0896

• CW Dunn, M Howison, and F Zapata (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. http://dx.doi.org/10.1186/1471-2105-14-330

Here is the original description from that first paper:

In the first step, monophyly masking, all but one sequence were deleted in clades of sequences derived from the same taxon. The retained sequence was chosen at random. Paralogue pruning, the next step, consisted of identifying the maximally inclusive subtree that has no more than one sequence per taxon. This tree is then pruned away for further analysis, and the remaining tree is used as a substrate for another round of pruning. The process is repeated until the remaining tree has no more than one sequence per taxon. If there were multiple maximally inclusive subtrees of the same size in a given round, then they were all pruned away at the same time.

Because treeprune does not require any information beyond the gene trees, such as a species tree, it is appropriate for processing gene trees in preparation for construction of supermatrices for phylogenomic inference.

The treeprune code presented here was derived directly from the Agalma code, and includes the following modifications:

• Code was update from python 2 to python 3
• Only the code and dependencies relevant to treeprune were retained, greatly reducing dependencies
• Code was added so that treeprune can be used as a standalone tool rather than as part of the agalma pipeline.
• Monophyly masking has been renamed monophyly_prune to be consistent with the tern paralogy_prune, and to reflect the fact that it is pruning and not masking.

Example of using treeprune within python

Both monophyly_prune and paralogy_prune are available from phylopytho.treeprune, and can be used as follows. A Google Colab notebook based on this example is also available.

from dendropy import Tree
from phylopytho import treeprune

# Build the tree
tree_text = "(((((((A@1,B@1),C@1),A@2),A@4),(B@2,B@3)),C@2),A@3);"
t = Tree.get_from_string( tree_text, schema='newick', rooting='force-rooted' )
t.print_plot()

# Perform monophyly pruning
t = treeprune.monophyly_prune(t)
t.print_plot()

# Perform paralogy pruning
pruned_trees = list()
treeprune.paralogy_prune(t, pruned_trees)
print(f'Number of pruned subtrees: {len(pruned_trees)}')

# Print the trees
for pruned_tree in pruned_trees:
  # Can only print trees with more than 1 tip
  if len(pruned_tree) > 1:
    pruned_tree.print_plot()
  else:
    print("single taxon")

# Print the sets of tips in each tree
for pruned_tree in pruned_trees:
  tips = treeprune.get_taxa(pruned_tree.leaf_nodes())
  print(tips)

Example of command line treeprune analysis

treeprune can also be used at the command line as a stand-alone script when the phylopytho module is installed. By default, it applies both monophyly_prune and paralogy_prune.

To give it a try, in the root of this repository first activate the conda environment as described above, and then run:

treeprune phylopytho/data/gene_trees.tre pruned_trees.tre

This will generate a set of pruned trees from an example set of trees included in the module.

To get a full description of options run:

treeprune --help

Development

Setting up the development environment

To setup the development environment:

conda activate phylopytho
pip install .[dev]
pre-commit install

This creates hooks that will run black and flake8 upon each commit.

Running tests

In the root of this repository, run:

conda activate phylopytho
python -m pytest