Software

BDMS

A Python package for tree simulation from general birth-death-mutation-sampling processes

docs, repo

multidms

A Python package that extends global epistasis models for joint estimation from deep mutational scans from multiple backgrounds

docs, repo, paper

mushi

A Python package for mutation spectrum history inference

docs, repo, paper

mutyper

A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs

docs, repo, paper

gctree

A Python package for phylogenetic inference of genotype-collapsed trees

docs, repo, paper