Software
Tools we build and maintain for phylogenetic and population-genomic inference. All are open source on GitHub.
popai
A python package for demographic model selection. This is currently in development. Check it out, and let us know what you think!
phyloGAN
phyloGAN is a Generative Adversarial Network (GAN) that infers phylognetic relationships. phyloGAN takes as input a concatenated alignments, or a set of gene alignments, and then infers a phylogenetic tree either considering or ignoring gene tree heterogeneity.
Smith & Hahn, 2023 — Bioinformatics
delimitR
delimitR delimits species while considering population-level processes like gene flow, and can also be used to compare demographic models using Random Forests and the Site Frequency Spectrum.
Smith & Carstens, 2020 — Evolution
Ortholog Extraction
A series of scripts to extract orthologs from larger gene family trees, including a novel branch-cutting method.
Smith et al., 2022 — Molecular Biology and Evolution
dupcoal
dupcoal is a simulator that simulates gene trees under duplication, loss, and coalescence. dupcoal allows for copy-number hemiplasy, unlike many other such simulators.
Mishra et al. — bioRxiv