biopython
Freely available tools for computational molecular biology.
Latest release 1.78 - Updated - 2.7K stars
tskit
The tree sequence toolkit.
Latest release 0.3.6 - Updated - 62 stars
treeswift
TreeSwift: Fast tree module for Python 2 and 3
Latest release 1.1.15 - Updated - 35 stars
ete3
Python package for building, comparing, annotating, manipulating and visualising trees. It provid...
Latest release 3.1.2 - Updated - 506 stars
hyphy-vision
HyPhy's visual interface
Latest release 2.9.1 - Updated - 4 stars
ete3
A Python Environment for (phylogenetic) Tree Exploration
Latest release 3.1.2 - Updated
gtdbtk
A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Latest release 1.5.0 - Updated - 179 stars
hyphy-python
HyPhy package interface library
Latest release 0.1.10 - Updated - 116 stars
@neherlab/nextclade
Clade assignment, mutation calling, and sequence quality checks
Latest release 0.14.2 - Updated - 62 stars
tskit
Toolkit for storing and processing large-scale genetic genealogies.
Latest release 0.3.5 - Updated - 62 stars
RNeXML
Semantically Rich I/O for the 'NeXML' Format
Latest release 2.4.4 - Updated - 14 stars
phylobase
Base Package for Phylogenetic Structures and Comparative Data
Latest release 0.8.10 - Updated - 12 stars
phydms
Phylogenetic analyses informed by deep mutational scanning data.
Latest release 2.4.1 - Updated - 11 stars
phylo-treetime
Maximum-likelihood phylodynamic inference
Latest release 0.8.1 - Updated - 94 stars
buddysuite
BuddySuite is a collection of command line utilities written in Python for working with biologica...
Latest release 1.3.0 - Updated - 71 stars
@nextstrain/nextclade
Clade assignment, mutation calling, and sequence quality checks
Latest release 0.14.2 - Updated - 62 stars
phylotree
Interactive viewer of phylogenetic trees
Latest release v0.1.5 - Published - 60 stars
baltic
Lightweight package for analyzing, manipulating and visualizing annotated phylogenetic trees
Latest release 0.1.6 - Updated - 42 stars
treesapp
TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.
Latest release 0.11.0 - Updated - 14 stars
python-nexus
A nexus (phylogenetics) file reader (.nex, .trees)
Latest release 2.1.0 - Updated - 7 stars
phylopath
Perform Phylogenetic Path Analysis
Latest release 1.1.2 - Updated - 7 stars
rncl
An Interface to the Nexus Class Library
Latest release 0.8.4 - Updated - 6 stars
nLTT
Calculate the NLTT Statistic
Latest release 1.4.3 - Updated - 3 stars
DendroPy
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, proc...
Latest release 4.5.2 - Updated
biopython
Biopython is a collection of freely available Python tools for computational molecular biology
Latest release 1.77 - Updated - 2.7K stars
HyPhy
HyPhy package interface library
Latest release 0.1.3 - Published - 116 stars
phylopandas
Pandas for phylogenetics
Latest release 0.8.0 - Updated - 36 stars
trifusion
Streamlining phylogenomic data gathering, processing and visualization
Latest release 1.0.2 - Updated - 33 stars
phylorank
Assigns taxonomic ranks based on evolutionary divergence.
Latest release 0.1.10 - Updated - 13 stars
qiime-tools
Useful additions to the QIIME analysis pipeline including tools for data visualization and cluste...
Latest release 1.1.2 - Updated - 11 stars
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