Phylogenetics Python Packages

biopython

Official git repository for Biopython (originally converted from CVS)

9M 5K 2K

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.

261K 878 227

tskit

Population-scale Ancestral Recombination Graph (ARG) library

99K 184 84

cogent3

Comparative Genomics Toolkit 3

23K 135 67

clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

11K 89 5

phykit

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

9K 85 9

phylo-treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

8K 251 60

nj-py

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

3K 2 0

itolapi

Python API for the Interactive Tree of Life (iTOL)

3K 38 11

taxoniumtools

A tool for exploring large trees in the browser

3K 132 28

trisicell

No description available

3K 14 2

phylopypruner

Tree-based orthology inference with functionality for reducing contamination

3K 8 1

diverse-seq

Tools for analysis of sequence divergence

2K 15 4

treesapp

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

2K 26 4

teiphy

A Python package for converting TEI XML collations to NEXUS, BEAST 2.7 XML, and other formats

2K 22 5

chronumental

Estimating time trees from very large phylogenies

2K 28 7

gtdbtk

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

2K 598 98

plastburstalign

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

2K 1 0

pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

2K 39 7

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).

1K 122 33