ESL-PSC Toolkit: a graphical software environment for linking shared genetic changes to convergent phenotypes

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ID: 324730
2026
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Abstract
Abstract Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolutionary Sparse Learning with Paired Species Contrast (ESL-PSC) is an approach to identify genes and sites associated with convergent traits from aligned sequences by fitting sparse predictive models to phylogenetically informed species contrasts. However, practical use of ESL-PSC currently requires substantial command-line fluency for data assembly, species-pair design, execution, and output interpretation. Here we present an integrated ESL-PSC analysis environment (ESL-PSC Toolkit) centered on a graphical user interface (GUI). ESL-PSC Toolkit is designed to assist users from experimental design through data interpretation without requiring extensive technical expertise. It supports guided input validation, interactive tree-based pair selection, command preview, live execution, post-run exploration of ranked genes and aligned sites, a complementary substitution-counting method, and analysis of continuous quantitative convergent traits. The computational backend has been reimplemented in Rust with many performance optimizations and parallelism, greatly reducing runtime for most analyses and enabling cross-platform packaged distributions. Downloadable GUI and CLI toolkit software packages for Mac, Windows, and Linux are available at https://github.com/kumarlabgit/ESL-PSC/releases/latest
Reference Key
openalex_W7162686299 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors John B. Allard, Sudhir Kumar
Journal molecular biology and evolution
Year 2026
DOI
10.1093/molbev/msag205
URL
https://doi.org/10.1093/molbev/msag205
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