Software and Resources
CAAStools, a toolbox to identify and test convergent amino acid substitutions
CAAStools is a lightweight suite of Python tools to identify and validate Convergent Amino Acid Substitutions (CAAS) by scanning multiple sequence alignments (MSA) of orthologous proteins (or translated nucleotides) and testing whether species with divergent trait values converge to different amino acids. It is designed to scale CAAS discovery to proteome-wide analyses, and includes modules to detect CAAS in a single MSA, resample phenotype groups (random, phylogeny-restricted, or Brownian-motion based), and run bootstrap validation to estimate empirical support for candidate sites.
Fabio Barteri, Alejandro Valenzuela, Xavier Farré, David de Juan, Gerard Muntané, Borja Esteve-Altava, and Arcadi Navarro. 2023. “CAAStools: A Toolbox to Identify and Test Convergent Amino Acid Substitutions.” Bioinformatics 39 (10): btad623. https://doi.org/10.1093/bioinformatics/btad623.
The Primate Genome-Phenome Archive
The Primate Genome-phenome Archive (PGA) is a comprehensive repository of 263 complex traits across 224 primate species, each with a predicted genetic background inferred through comparative methods. These predictions draw on convergent amino acid substitution analyses (Barteri et al., 2023) and relative evolutionary rates (RER) estimations (Kowalczyk et al., 2019), providing valuable insights into the molecular underpinnings of primate trait evolution. The findings presented here originate from the work of Valenzuela et al. (2025), 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 GitHub repository.
⬇️ Visit the repositoryValenzuela, Alejandro*, Fabio Barteri*, Lukas Kuderna, Joseph Orkin, Jean Boubli, Amanda Melin, Hafid Laayouni, et al. Posted September 8, 2025. “A Phylogenetic Protein-Coding Genome-Phenome Map of Complex Traits across 224 Primate Species.” bioRxiv. https://doi.org/10.1101/2025.09.08.674744.
