Official git repository for Biopython (originally converted from CVS)
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Updated
Jul 1, 2024 - Python
Official git repository for Biopython (originally converted from CVS)
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.
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Population-scale genomics
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
Comparative Genomics Toolkit 3
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).
Streamlining phylogenomic data gathering, processing and visualization
Pandas DataFrames for phylogenetics
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
A tool for drawing ANI clustermap between all-vs-all microbial genomes
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Nextstrain build for mpox virus
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Python API for the Interactive Tree of Life (iTOL)
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.
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