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.

tskit

Population-scale Ancestral Recombination Graph (ARG) library

cogent3

Comparative Genomics Toolkit 3

phykit

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

nj-py

Neighbor-Joining phylogenetic tree inference. Auto-detects DNA/protein, supports multiple substitution models and bootstrap.

phylo-treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

diverse-seq

Tools for analysis of sequence divergence

itolapi

Python API for the Interactive Tree of Life (iTOL)

taxoniumtools

Generate files for taxonium

trisicell

No description available

gtdbtk

A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

teiphy

Converts TEI XML collations to NEXUS and other formats

pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

treesapp

TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.

scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

chronumental

Estimating time trees from very large phylogenies

gctree

phylogenetic inference of genotype-collapsed trees

plastburstalign

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

pear-ebi

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

asymmetree

Simulator for species and gene trees with asymmetric evolution rates

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).

bionick

Software for manipulating Newick strings and adding phylogenies to Matplotlib visuals.