phylogenetics topic
GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
IQ-TREE
Efficient phylogenomic software by maximum likelihood
hyphy
HyPhy: Hypothesis testing using Phylogenies
treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
tskit
Population-scale genomics
phylopandas
Pandas DataFrames for phylogenetics
phyx
phylogenetics tools for linux (and other mostly posix compliant) computers
CAFE
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
CAFE5
Version 5 of the CAFE phylogenetics software
epa-ng
Massively parallel phylogenetic placement of genetic sequences