Molecular Evolution Python Packages

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.

phydms

phylogenetic analyses informed by deep mutational scanning data

gains

Genetic Algorithm for Identifying Novel Structures (GAINS)

fastdtlmapper

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

cafeplotter

A tool for plotting CAFE5 gene family expansion/contraction result

predsim

Command-line tool for simulating predictive datasets from MrBayes' output.

mgcplotter

Microbial Genome Circular plotting tool using Circos