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

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 and expertise for data assembly, species-pair design, 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, 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.