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<!DOCTYPE html>
<html lang="it">
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<title>Fabio Barteri – Macroevolutionary Genomics</title>
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<article class="card card-large">
<h2 class="card-title">Software and Resources</h2>
<!-- CAAStools-->
<h3>CAAStools, a toolbox to identify and test <strong>convergent amino acid substitutions</strong></h3>
<figure class="image-figure" style="margin-bottom:20px;">
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<img class="zoomable" src="img/caastools.fig1.jpg" data-full="img/caastools.fig1.jpg" alt="CAAStools figure" style="width:100%; height:auto;" />
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<figcaption class="image-caption">
<strong>Fig 1: </strong>CAAStools architecture and workflow (<a href="https://doi.org/10.1093/bioinformatics/btad623" target="_blank" rel="noopener noreferrer">Barteri et al., 2023</a>)
</figcaption>
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<p>
<a href="http://github.com/linudz/caastools" target="_blank" rel="noopener noreferrer"><strong>CAAStools</strong></a>
is a lightweight suite of <strong>Python</strong> tools to identify and validate
<strong>Convergent Amino Acid Substitutions (CAAS)</strong> by scanning
<strong>multiple sequence alignments (MSA)</strong> of orthologous proteins (or translated nucleotides) and testing whether
species with <strong>divergent trait values</strong> converge to different amino acids.
It is designed to scale CAAS discovery to <strong>proteome-wide</strong> analyses, and includes modules to
<strong>detect CAAS</strong> in a single MSA, <strong>resample phenotype groups</strong> (random, phylogeny-restricted, or
<strong>Brownian-motion</strong> based), and run <strong>bootstrap validation</strong> to estimate empirical support for candidate sites.
</p>
<p class="selected-publication">
<strong>Fabio Barteri</strong>, Alejandro Valenzuela, Xavier Farré, David de Juan, Gerard Muntané, Borja Esteve-Altava, and Arcadi Navarro.
<strong>2023</strong>. “<strong>CAAStools: A Toolbox to Identify and Test Convergent Amino Acid Substitutions</strong>.”
<em>Bioinformatics</em> 39 (10): btad623.
<a href="https://doi.org/10.1093/bioinformatics/btad623" target="_blank" rel="noopener noreferrer">https://doi.org/10.1093/bioinformatics/btad623</a>.
</p>
<p>
<a href="http://github.com/linudz/caastools" target="_blank" rel="noopener noreferrer">⬇️ <strong>Download from GitHub</strong></a>
</p>
<h3 class="article">The Primate Genome-Phenome Archive</h3>
<p>The Primate Genome-phenome Archive (PGA) is a comprehensive repository of <strong>263 complex traits</strong> across <strong>224 primate species</strong>, each with a predicted genetic background inferred through comparative methods. These predictions draw on convergent amino acid substitution analyses (<a href="https://doi.org/10.1093/bioinformatics/btad623" target="_blank" rel="noopener noreferrer">Barteri et al., 2023</a>) and relative evolutionary rates (RER) estimations (<a href="https://doi.org/10.1093/bioinformatics/btz468" target="_blank" rel="noopener noreferrer">Kowalczyk et al., 2019</a>), providing valuable insights into the molecular underpinnings of primate trait evolution. The findings presented here originate from the work of <a href="https://www.biorxiv.org/content/10.1101/2025.09.08.674744v1" target="_blank" rel="noopener noreferrer">Valenzuela et al. (2025)</a>, which highlights significant patterns of convergence and divergence among diverse primate lineages. The database is openly accessible on GitHub in a standardized format, allowing for programmatic data retrieval and integration. Comprehensive documentation, including a detailed changelog, is available on the <a href="https://github.com/pgarchive/data" target="_blank" rel="noopener noreferrer">GitHub repository</a>.</p> </div>
<a href="http://pgarchive.github.io" target="_blank" rel="noopener noreferrer">⬇️ <strong>Visit the repository</strong></a>
</p>
<p class="selected-publication">
Valenzuela, Alejandro*, <strong>Fabio Barteri*</strong>, Lukas Kuderna, Joseph Orkin, Jean Boubli, Amanda Melin, Hafid Laayouni, et al.
<strong>Posted September 8, 2025</strong>. “<strong>A Phylogenetic Protein-Coding Genome-Phenome Map of Complex Traits across 224 Primate Species</strong>.”
<em>bioRxiv</em>.
<a href="https://doi.org/10.1101/2025.09.08.674744" target="_blank" rel="noopener noreferrer">https://doi.org/10.1101/2025.09.08.674744</a>.
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<h2 class="card-title">Future developments</h2>
<p>
As of January 2026, I am working on improving CAAStools and developing new algorithms to test phenotypic variation within a phylogeny. For more information, please <a href="contacts.html">contact me</a>.
</p>
<a href="http://github.com/linudz/caastools" target="_blank" rel="noopener noreferrer"><img src="img/caastools.logo.png" style="width:60%; height:auto; margin-bottom:20px;" /></a>
<a href="http://pgarchive.github.io" target="_blank" rel="noopener noreferrer"><img src="img/pga.logo.png" style="width:60%; height:auto; margin-bottom:20px;" /></a>
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