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The Top 23 Python Phylogenetics Open Source Projects

Open source projects categorized as Python 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
Vcf2phylip ⭐ 216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
most recent commit 10 months ago
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36most recent commit 3 months agopypi tskit} Downloads
Buddysuite ⭐ 105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
total releases 18most recent commit 2 years 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
Trifusion ⭐ 61
Streamlining phylogenomic data gathering, processing and visualization
total releases 35most recent commit 6 years ago
R2g ⭐ 49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
dependent packages 1total releases 6most recent commit 3 years agopypi r2g} Downloads
Clipkit ⭐ 44
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
total releases 34most recent commit 5 months ago
Phykit ⭐ 44
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
total releases 50most recent commit 4 months ago
Phylopandas ⭐ 39
Pandas DataFrames for phylogenetics
dependent packages 4total releases 13most recent commit 5 years agopypi phylopandas} Downloads
Aniclustermap ⭐ 38
A tool for drawing ANI clustermap between all-vs-all microbial genomes
total releases 5most recent commit 6 months ago
Mpox ⭐ 37
Nextstrain build for mpox virus
most recent commit 3 months ago
Favites ⭐ 35
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
most recent commit 5 months ago
Itolapi ⭐ 31
Python API for the Interactive Tree of Life (iTOL)
dependent packages 4total releases 20most recent commit 3 months agopypi itolapi} Downloads
Orthoevolution ⭐ 28
An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵
total releases 2most recent commit a year ago
Busco_phylogenomics ⭐ 26
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
most recent commit 6 months ago
Q2 Qemistree ⭐ 24
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
most recent commit a year ago
Phylociraptor ⭐ 23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
most recent commit 5 months ago
Ghost Tree ⭐ 23
creating hybrid-gene phylogenetic trees for diversity analyses
most recent commit 2 years ago
Treesapp ⭐ 22
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
most recent commit a year ago
The 10 Most Depended On Python 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
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36latest release October 10, 2023most recent commit 3 months agopypi tskit} Downloads
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
Itolapi ⭐ 31
Python API for the Interactive Tree of Life (iTOL)
dependent packages 4total releases 20latest release January 15, 2023most recent commit 3 months agopypi itolapi} Downloads
Phylopandas ⭐ 39
Pandas DataFrames for phylogenetics
dependent packages 4total releases 13latest release September 26, 2019most recent commit 5 years agopypi phylopandas} Downloads
Cogent3 ⭐ 79
Comparative Genomics Toolkit 3
dependent packages 2total releases 18latest release September 22, 2023most recent commit 3 months agopypi cogent3} Downloads
R2g ⭐ 49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
dependent packages 1total releases 6latest release November 23, 2020most recent commit 3 years agopypi r2g} Downloads
Gtdbtk ⭐ 383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48latest release July 11, 2022most recent commit 5 months agopypi gtdbtk} Downloads
The 10 Latest Releases In Python Phylogenetics Open Source Projects
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
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 4 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 4 months ago
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36latest release October 10, 2023most recent commit 3 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
Gctree ⭐ 12
GCtree: phylogenetic inference of genotype-collapsed trees
total releases 15latest release August 10, 2023most recent commit 3 months ago
Scphylo Tools ⭐ 5
a python toolkit for single-cell tumor phylogenetic analysis
total releases 5latest release July 26, 2023most recent commit 4 months ago
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