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The Top 23 Python Bioinformatics Phylogenetics Open Source Projects

Open source projects categorized as Python Bioinformatics Phylogenetics
Categories > Data Processing > Bioinformatics
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
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
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
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
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
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
Ghost Tree ⭐ 23
creating hybrid-gene phylogenetic trees for diversity analyses
most recent commit 2 years ago
Phylociraptor ⭐ 23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
most recent commit 5 months ago
Treesapp ⭐ 22
A Python package for gene-centric taxonomic and functional classification using phylogenetic placement
most recent commit a year ago
Orthosnap ⭐ 16
a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
total releases 6most recent commit 4 months ago
Lineage Designation ⭐ 16
Official place for proposals and details around monkeypox virus lineage designations
most recent commit 9 months ago
Topiary ⭐ 15
Python framework for doing ancestral sequence reconstruction
total releases 1most recent commit a year ago
Wqfm 2020 ⭐ 13
wQFM implementation in Java
most recent commit a year ago
Cafeplotter ⭐ 13
A tool for plotting CAFE5 gene family expansion/contraction result
most recent commit 7 months ago
Phylotoast ⭐ 12
Tools for phylogenetic data analysis including visualization and cluster-computing support.
total releases 3most recent commit 2 years ago
Avp ⭐ 12
Automatic evaluation of HGTs
most recent commit 5 months ago
The 6 Most Depended On Python Bioinformatics 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
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
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 Bioinformatics 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
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
Scphylo Tools ⭐ 5
a python toolkit for single-cell tumor phylogenetic analysis
total releases 5latest release July 26, 2023most recent commit 4 months ago
Trisicell ⭐ 9
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
total releases 25latest release July 21, 2023most recent commit 4 months ago
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
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
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