diff --git a/404.html b/404.html
index f0866ae..d7120d0 100644
--- a/404.html
+++ b/404.html
@@ -100,7 +100,7 @@ <h1>Page not found (404)</h1>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 3b80ef7..ac6dcf0 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -274,7 +274,7 @@ <h1>License</h1>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/articles/index.html b/articles/index.html
index 0d3cdfd..9b03210 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -74,7 +74,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/articles/v1_introduction.html b/articles/v1_introduction.html
index 3a0b190..8c2fd93 100644
--- a/articles/v1_introduction.html
+++ b/articles/v1_introduction.html
@@ -92,7 +92,7 @@ <h4 data-toc-skip class="author">Luca De
                         <h4 data-toc-skip class="author">Gianluca
 Ascolani</h4>
             
-            <h4 data-toc-skip class="date">March 26, 2024</h4>
+            <h4 data-toc-skip class="date">April 24, 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/BIMIB-DISCo/VERSO/blob/HEAD/vignettes/v1_introduction.Rmd" class="external-link"><code>vignettes/v1_introduction.Rmd</code></a></small>
       <div class="hidden name"><code>v1_introduction.Rmd</code></div>
@@ -148,7 +148,7 @@ <h2 id="debug">Debug<a class="anchor" aria-label="anchor" href="#debug"></a>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer>
diff --git a/articles/v2_running_VERSO.html b/articles/v2_running_VERSO.html
index 987d99b..18fdc96 100644
--- a/articles/v2_running_VERSO.html
+++ b/articles/v2_running_VERSO.html
@@ -92,7 +92,7 @@ <h4 data-toc-skip class="author">Luca De
                         <h4 data-toc-skip class="author">Gianluca
 Ascolani</h4>
             
-            <h4 data-toc-skip class="date">March 26, 2024</h4>
+            <h4 data-toc-skip class="date">April 24, 2024</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/BIMIB-DISCo/VERSO/blob/HEAD/vignettes/v2_running_VERSO.Rmd" class="external-link"><code>vignettes/v2_running_VERSO.Rmd</code></a></small>
       <div class="hidden name"><code>v2_running_VERSO.Rmd</code></div>
@@ -190,7 +190,7 @@ <h2 id="example-of-phylogenetic-inference-by-verso">Example of phylogenetic infe
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer>
diff --git a/authors.html b/authors.html
index f1da264..270b717 100644
--- a/authors.html
+++ b/authors.html
@@ -110,7 +110,7 @@ <h1 id="citation">Citation</h1>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/index.html b/index.html
index 1ecce84..6927d20 100644
--- a/index.html
+++ b/index.html
@@ -105,7 +105,7 @@
 <p>The R version of <em>VERSO</em> can be installed from Github. To do so, we need to install the R packages <em>VERSO</em> depends on and the devtools package.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># install VERSO dependencies</span></span>
-<span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="http://ape-package.ird.fr/" class="external-link">"ape"</a></span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"ape"</span><span class="op">)</span></span>
+<span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://github.com/emmanuelparadis/ape" class="external-link">"ape"</a></span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"ape"</span><span class="op">)</span></span>
 <span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://github.com/RfastOfficial/Rfast" class="external-link">"Rfast"</a></span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"Rfast"</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># install VERSO library</span></span>
@@ -169,7 +169,7 @@ <h2 data-toc-skip>Developers</h2>
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer>
diff --git a/pkgdown.yml b/pkgdown.yml
index 820ebef..45eae9b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,8 +1,8 @@
 pandoc: 3.1.1
-pkgdown: 2.0.7.9000
-pkgdown_sha: 676cf1dce39e4dc5aa1bcb671b1e14e992589a0a
+pkgdown: 2.0.9.9000
+pkgdown_sha: 4e7ffec191b6e42d0e3dd718e5719ddf66f5eef9
 articles:
   v1_introduction: v1_introduction.html
   v2_running_VERSO: v2_running_VERSO.html
-last_built: 2024-03-26T07:26Z
+last_built: 2024-04-24T07:31Z
 
diff --git a/reference/VERSO.html b/reference/VERSO.html
index 8ad7ec3..00abad6 100644
--- a/reference/VERSO.html
+++ b/reference/VERSO.html
@@ -191,7 +191,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/reference/index.html b/reference/index.html
index 639867f..232f796 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -89,7 +89,7 @@ <h2 id="all-functions">All functions <a href="#all-functions" class="anchor" ari
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/reference/inference.html b/reference/inference.html
index b01cac9..1c7c90b 100644
--- a/reference/inference.html
+++ b/reference/inference.html
@@ -89,7 +89,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/reference/variants.html b/reference/variants.html
index 1f8ee0a..12a8845 100644
--- a/reference/variants.html
+++ b/reference/variants.html
@@ -97,7 +97,7 @@ <h2>Value</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>
diff --git a/reference/write.newick.tree.html b/reference/write.newick.tree.html
index f38a2b5..77a9f60 100644
--- a/reference/write.newick.tree.html
+++ b/reference/write.newick.tree.html
@@ -103,7 +103,7 @@ <h2>Examples</h2>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.9000.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.9000.</p>
 </div>
 
       </footer></div>