Molecular Evolution Python Packages

msasim

Backend C++ code for the Sailfish MSA simulation library using the Pybind11 framework

cogent3

Comparative Genomics Toolkit 3

stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

zombi2

A Python library for simulating the evolution of species, genomes, sequences and traits

phydms

phylogenetic analyses informed by deep mutational scanning data

gains

project that enables molecular design and computational screening of small molecules

fastdtlmapper

Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method

predsim

Simulate predictive datasets from MrBayes' output

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

mgcplotter

Microbial Genome Circular plotting tool for comparative genomics using Circos

zombi2-core

A Python library for simulating the evolution of species, genomes, sequences and traits