John B. Allard | Searcharxiv

arXiv2026

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 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/John-Allard/ESL-PSC/releases/latest.

q-bio.PE↗

arXiv2025

Treemble: A Graphical Tool to Generate Newick Strings from Phylogenetic Tree Images

Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the machine-readable newick format. There are thus thousands of published trees in the scientific literature that are unavailable for follow-up analyses, comparisons, supertree construction, etc. Experts can easily read such diagrams, but the manual construction of a newick string is prohibitively laborious. Previous attempts to semi-automate the reading of tree images relied on image processing techniques. These quickly encounter difficulties with typical published tree diagrams that contain various graphical elements that overlap the branches, such as error bars on internal nodes. Here we introduce Treemble, a user-friendly desktop application for generating newick strings from tree images. The user simply clicks to mark node locations, and Treemble algorithmically assembles the tree from the node coordinates alone. Tip nodes can be automatically detected and marked. Treemble also facilitates the automatic reading of tip name labels and can handle both rectangular and circular trees. Treemble is a native desktop application for both MacOS and Windows, and is freely available and fully documented at treemble.org.

q-bio.PE↗