phylogenomics topic
anvio
An analysis and visualization platform for 'omics data
IQ-TREE
Efficient phylogenomic software by maximum likelihood
nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
SynNet-Pipeline
Workflow for Building Microsynteny Networks
ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
get_phylomarkers
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
BUSCO_phylogenomics
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
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.
CafePlotter
A tool for plotting CAFE5 gene family expansion/contraction result