Phylogenetics Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

ete3

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

phylo-treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

tskit

Population-scale Ancestral Recombination Graph (ARG) library

rapidtrees

A blazing fast rust-based tool for tree distances.

phykit

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

msasim

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

cogent3

Comparative Genomics Toolkit 3

zombi2

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

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

diverse-seq

Tools for analysis of sequence divergence

taxoniumtools

A tool for exploring large trees in the browser

itolapi

Python API for the Interactive Tree of Life (iTOL)

phylokit-mcp

MCP server for phylogenetic inference over IQ-TREE 3 (through piqtree) — never returns a topology without its bootstrap support

hyphlow

A GUI-based bioinformatics pipeline for preparing, running, and summarizing HyPhy evolutionary selection analyses.

chronumental

Estimating time trees from very large phylogenies

phylozoo

PhyloZoo: a Python package for working with phylogenetic networks and related evolutionary datatypes

pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

baltic

baltic - Backronymed Adaptable Lightweight Tree vIsualisation Code for molecular phylogeny manipulation, analysis and visualisation.

trisicell

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

phylopypruner

Tree-based orthology inference with functionality for reducing contamination

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

figtreekit

Programmatic styling of phylogenetic trees for FigTree visualization