An analysis and visualization platform for 'omics data

Efficient phylogenomic software by maximum likelihood

💾 📃 "Reads to report" for public health and clinical microbiology

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

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

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

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

Workflow for Building Microsynteny Networks

Hybridization detection using phylogenetic invariants

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.

a broadly applicable tool for automated gene identification and retrieval

Phylogenetic Likelihood Library

A tool for plotting CAFE5 gene family expansion/contraction result

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

An ultrafast and memory efficient tool for phylogenomics

An R package to infer and analyze synteny networks from protein sequences

a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

PHANTASM: PHylogenomic ANalyses for the TAxonomy and Systematics of Microbes