HyPhy

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

1 shared topic • 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

1 shared topic • 2 shared operations

Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c

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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

1 shared topic • 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

1 shared topic • 2 shared operations