Evolutionary Biology Python Packages

pypop-genomics

PyPop: Python for Population Genomics

phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

phylo3d-trait

Interactive 3D phylogenetic tree visualizer for continuous trait evolution and supplied ancestral-state estimates; standalone WebGL2 HTML.

graphfla

A graph-based python framework for fitness landscape analysis

phylocartoplot

PhyloGeoPlot: a python toolkit for phylogeographic visualization linking phylogenetic and geographic data

phylogeoplot

PhyloGeoPlot: a python toolkit for phylogeographic visualization linking phylogenetic and geographic data

jlsteenwyk-biokit

a versatile toolkit for processing and analyzing diverse types of sequence data

orthofisher

a broadly applicable tool for automated gene identification and retrieval

orthosnap

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

aegis-sim

Numerical model for life history evolution of age-structured populations

mpi-age-aegis

Numerical model for life history evolution of age-structured populations