A python package for demographic model selection. This is currently in development. Check it out, and let us know what you think!

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.

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 and Carstens, 2020).

A series of scripts to extract orthologs from larger gene family trees, including a novel branch-cutting method (Subtree Extraction, SE; Smith et al., 2022).

dupcoal is a simulator that simulates gene trees under duplication, loss, and coalescence. dupcoal allows for copy-number hemiplasy, unlike many other such simulators.