Phylogenetics Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

tskit

Population-scale Ancestral Recombination Graph (ARG) library

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.

phylo-treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

cogent3

Comparative Genomics Toolkit 3

phykit

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

nj-py

Neighbor Joining in rust, with python and JS/WASM wrappers

itolapi

Python API for the Interactive Tree of Life (iTOL)

phylozoo

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

phylopypruner

Tree-based orthology inference with functionality for reducing contamination

diverse-seq

Tools for analysis of sequence divergence

baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

taxoniumtools

A tool for exploring large trees in the browser

trisicell

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

gtdbtk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

treesapp

A Python package for gene-centric taxonomic and functional classification using phylogenetic placement

chronumental

Estimating time trees from very large phylogenies

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

plastburstalign

A Python tool to extract and align genes, introns, and intergenic spacers across thousands of plastid genomes using associative arrays

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

physquirrel

Squirrel: a Python package for reconstructing level-1 phylogenetic networks from sequence alignments or four-leaved networks

pear-ebi

Calculates distances of trees in large collections. Embeds distances and plot the embeddings with dynamic interfaces.