PAML

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 • 3 shared operations

PhyloBayes — Bayesian MCMC phylogenetic inference software using infinite mixture models (CAT, CAT-GTR) of amino acid or nucleotide substitution. Runs parallel MCMC chains, assesses convergence with b

2 shared topics • 3 shared operations

ASTRAL — fast species tree estimation from unrooted gene trees under the multi-species coalescent model. Handles incomplete lineage sorting (ILS) in phylogenomic datasets with hundreds of species and

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

TreeTime — maximum likelihood molecular clock inference, ancestral sequence reconstruction, and phylodynamic analysis from time-stamped phylogenies. Infers timetrees by iteratively optimizing ancestra

2 shared topics • 2 shared operations