PyPop: Python for Population Genomics

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

MSEABOARD: An open-source, web-based dashboard for interactive visualization and analysis of multiple sequence alignments, phylogenetic trees, protein structures, distance matrices and associated data.

Personal website - computational molecular evolution & biopipelines

Computer vision model to detect drosophila eggs from full caps using a novel technique called "Tiling"

Breitman Lab website

This repository contains Python and NetLogo simulations based on the paper "The conditional defector strategies can violate the most crucial supporting mechanisms of cooperation" (Scientific Reports, 2022). The models explore evolution of cooperation, conditional defection, and mechanisms like kin selection, spatial structure, and punishment.

Supporting code for a study on the phylogeography of the common gartersnake (Thamnophis sirtalis)

Create, modify and analyse phylogenetic trees in R

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

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

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

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

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

This repository provides an easy-to-use Python-based pipeline for reconstructing phylogenetic trees from whole bacterial genomes. It automates the process of identifying orthologous single-copy genes, aligning sequences, trimming alignments, and generating a concatenated supermatrix ready for phylogenetic analysis. The pipeline requires only .fasta

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

Newick formatted (phylogenetic) trees

An R interface to the PLAZA database for plant comparative genomics

A workflow to simulate selective sweeps in SLiM and turn the results into images

Repo for the biological analyses performed on taxonomic quasi-prime peptides.