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Phylogenetics Python Packages

Python packages with the GitHub topic phylogenetics. Sorted by relevance, with stars and monthly downloads.
biopython
biopython

Official git repository for Biopython (originally converted from CVS)

8.6M 5K 2K
etetoolkit
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.

166K 876 226
tskit-dev
tskit

Population-scale Ancestral Recombination Graph (ARG) library

98K 183 83
cogent3
cogent3

Comparative Genomics Toolkit 3

25K 134 67
jlsteenwyk
phykit

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

12K 84 8
holmrenser
nj-py

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

11K 1 0
neherlab
phylo-treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction

9K 251 60
jlsteenwyk
clipkit

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

7K 89 5
HuttleyLab
diverse-seq

Tools for analysis of sequence divergence

5K 15 4
albertyw
itolapi

Python API for the Interactive Tree of Life (iTOL)

5K 37 11
theosanderson
taxoniumtools

Generate files for taxonium

4K 131 28
faridrashidi
trisicell

No description available

3K 14 2
Ecogenomics
gtdbtk

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

3K 593 97
jjmccollum
teiphy

Converts TEI XML collations to NEXUS and other formats

3K 21 5
evolbioinfo
pastml

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

3K 39 7
hallamlab
treesapp

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

3K 26 4
faridrashidi
scphylo-tools

A python toolkit for single-cell tumor phylogenetic analysis

2K 7 1
theosanderson
chronumental

Estimating time trees from very large phylogenies

2K 28 7
matsengrp
gctree

phylogenetic inference of genotype-collapsed trees

2K 18 2
michaelgruenstaeudl
plastburstalign

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

1K 1 0
AndreaRubbi
pear-ebi

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

1K 6 3
david-schaller
asymmetree

Simulator for species and gene trees with asymmetric evolution rates

1K 7 2
evogytis
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 119 33
DeadlineWasYesterday
bionick

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

857 0 0
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