a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

a broadly applicable tool for automated gene identification and retrieval

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

PyPop: Python for Population Genomics

Create, modify and analyse phylogenetic trees in R

a versatile toolkit for processing and analyzing diverse types of sequence data

Evolutionary simulation where agents age, reproduce, and eat each other

Reproducible Quantitative Methods for EEB

A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests and viral simulations at scale. Related manuscripts: https://doi.org/10.1111/2041-210X.14168 and https://doi.org/10.1038/s41467-025-60988-8

Two-Tier Ensemble Aggregation Gene Co-expression Network (TEA-GCN): Capturing tissue/condition-specific co-expression from large transcriptomic datasets

Newick formatted (phylogenetic) trees

HARE: Genetic Feature Enrichment Analysis Pipeline

Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

Software for analysing Many-Analysts' style data and generating the ManyEcoEvo project data

Source code for ManyEcoEvo Manuscript

Numerical model for life history evolution of age-structured populations

A Julia interface to the Paleobiology Database (PBDB) data service.