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 tool for drawing ANI clustermap between all-vs-all microbial genomes

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

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)

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

Python framework for doing ancestral sequence reconstruction

Python API for the Interactive Tree of Life (iTOL)