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The Top 23 Phylogenetics Open Source Projects

Open source projects categorized as Phylogenetics
Categories > Phylogenetics
Biopython ⭐ 3,918
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,373total releases 58most recent commit 3 months agopypi biopython} Downloads
Ete ⭐ 730
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.
dependent packages 150total releases 30most recent commit 3 months agopypi ete3} Downloads
Gtdbtk ⭐ 383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48most recent commit 5 months agopypi gtdbtk} Downloads
Raxml Ng ⭐ 339
RAxML Next Generation: faster, easier-to-use and more flexible
most recent commit 4 months ago
Beast2 ⭐ 228
Bayesian Evolutionary Analysis by Sampling Trees
most recent commit 4 months ago
Vcf2phylip ⭐ 216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
most recent commit 10 months ago
Mrbayes ⭐ 201
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
total releases 1most recent commit 7 months ago
Treetime ⭐ 196
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
dependent packages 3total releases 39most recent commit 3 months agopypi phylo-treetime} Downloads
Phangorn ⭐ 196
Phylogenetic analysis in R
dependent packages 68total releases 58most recent commit 3 months ago
Hyphy ⭐ 190
HyPhy: Hypothesis testing using Phylogenies
dependent packages 1total releases 8most recent commit 4 months agopypi hyphy-python} Downloads
Beast Mcmc ⭐ 166
Bayesian Evolutionary Analysis Sampling Trees
most recent commit 6 months ago
Phyml ⭐ 156
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
most recent commit 5 months ago
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36most recent commit 4 months agopypi tskit} Downloads
Iq Tree ⭐ 125
Efficient phylogenomic software by maximum likelihood
most recent commit 4 years ago
Usher ⭐ 112
Ultrafast Sample Placement on Existing Trees
most recent commit 6 months ago
Buddysuite ⭐ 105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
total releases 18most recent commit 2 years ago
Phyx ⭐ 100
phylogenetics tools for linux (and other mostly posix compliant) computers
most recent commit 5 months ago
Cafe5 ⭐ 100
Version 5 of the CAFE phylogenetics software
most recent commit a year ago
Taxonium ⭐ 90
A tool for exploring very large trees in the browser
total releases 80most recent commit 15 days ago
Cogent3 ⭐ 79
Comparative Genomics Toolkit 3
dependent packages 2total releases 18most recent commit 3 months agopypi cogent3} Downloads
Baltic ⭐ 74
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).
dependent packages 2total releases 12most recent commit 9 months agopypi baltic} Downloads
Cafe ⭐ 71
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
most recent commit 3 years ago
Epa Ng ⭐ 66
Massively parallel phylogenetic placement of genetic sequences
most recent commit 2 years ago
The 10 Most Depended On Phylogenetics Open Source Projects
Biopython ⭐ 3,918
Official git repository for Biopython (originally converted from CVS)
dependent packages 1,373total releases 58latest release February 13, 2023most recent commit 3 months agopypi biopython} Downloads
Phangorn ⭐ 196
Phylogenetic analysis in R
dependent packages 68total releases 58latest release January 23, 2023most recent commit 3 months ago
Phylobase ⭐ 16
An R package that provides a base S4 class for comparative methods, incorporating one or more trees and trait data
dependent packages 24total releases 15latest release March 01, 2020most recent commit 3 months ago
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36latest release October 10, 2023most recent commit 4 months agopypi tskit} Downloads
Beautier ⭐ 13
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
dependent packages 6total releases 14latest release November 02, 2023most recent commit 4 months ago
Python Nexus ⭐ 11
python-nexus - Generic nexus (.nex, .trees) reader/writer for python
dependent packages 5total releases 44latest release March 29, 2022most recent commit a year agopypi python-nexus} Downloads
Phylopandas ⭐ 39
Pandas DataFrames for phylogenetics
dependent packages 4total releases 13latest release September 26, 2019most recent commit 5 years agopypi phylopandas} Downloads
Itolapi ⭐ 31
Python API for the Interactive Tree of Life (iTOL)
dependent packages 4total releases 20latest release January 15, 2023most recent commit 4 months agopypi itolapi} Downloads
Light_phylogeny ⭐ 9
Light phylogeny API for Rust
dependent packages 4total releases 81latest release May 23, 2023most recent commit 3 months agocargo light_phylogeny} Downloads
The 10 Latest Releases In Phylogenetics Open Source Projects
Taxonium ⭐ 90
A tool for exploring very large trees in the browser
total releases 80latest release November 28, 2023most recent commit 15 days ago
Aniclustermap ⭐ 38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
total releases 5latest release November 07, 2023most recent commit 6 months ago
Beautier ⭐ 13
R package to generate the same BEAST2 XML parameter files as generated by BEAUti 2
dependent packages 6total releases 14latest release November 02, 2023most recent commit 4 months ago
Chronumental ⭐ 18
Estimating time trees from very large phylogenies
total releases 55latest release November 01, 2023most recent commit 6 months ago
Orthosnap ⭐ 16
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
total releases 6latest release October 24, 2023most recent commit 5 months ago
Phykit ⭐ 44
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
total releases 50latest release October 17, 2023most recent commit 5 months ago
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36latest release October 10, 2023most recent commit 4 months agopypi tskit} Downloads
Clipkit ⭐ 44
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
total releases 34latest release October 02, 2023most recent commit 5 months ago
Cogent3 ⭐ 79
Comparative Genomics Toolkit 3
dependent packages 2total releases 18latest release September 22, 2023most recent commit 3 months agopypi cogent3} Downloads
Teiphy ⭐ 8
A Python package for converting TEI XML collations to NEXUS and other formats
total releases 7latest release September 12, 2023most recent commit 4 months ago
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