Mash

ParSNP — rapid core-genome alignment and SNP detection for closely related microbial genomes (bacteria, archaea). Part of the HARVEST suite alongside HarvestTools and Gingr. Aligns hundreds of whole-g

2 shared topics • 3 shared operations

BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel

2 shared topics • 2 shared operations

ClonalFrameML detects recombination (horizontal gene transfer) in bacterial whole-genome alignments using maximum likelihood inference. It takes a Newick phylogenetic tree and FASTA/XMFA alignment, th

2 shared topics • 2 shared operations

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

2 shared topics • 2 shared operations

TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a Java-based software package for genome-wide association studies (GWAS), population genetics, and linkage disequilibrium analysis. Su

2 shared topics • 2 shared operations