FGTpartitioner
FGTpartitioner: A rapid method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets - Published in JOSS (2020)
phylofisher
PhyloFisher is a software package written in Python3 that can be used for the creation, analysis, and visualization of phylogenomic datasets that consist of eukaryotic protein sequences.
clipkit
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
orthofisher
a broadly applicable tool for automated gene identification and retrieval
syntenet
An R package to infer and analyze synteny networks from protein sequences
aniclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
whole-genome-sequencing-and-comparative-genomics-of-human-lung-streptococcal-isolates
Genomic sequencing, phylogenetic analysis and comparative genomics by pan-genome analysis of human distal lung Streptococcus isolates.
https://github.com/cdcgov/microbetrace
The Visualization Multitool for Molecular Epidemiology and Bioinformatics