BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.

This package includes the following plugins: - BDSKY: Birth-death skyline model - BEASTLabs: Laboratory for new BEAST development - BEASTCLASSIC: Classic BEAST 1.x models - BICEPS: Bayesian Integration of Coalescent and Epidemiological Processes - bModelTest: Bayesian model selection for nucleotide substitution models - CCD: Conditional clade distributions - CodonSubstModels: Codon substitution models - FastRelaxedClockLogNormal: Fast relaxed clock with log-normal distribution - feast: Fast End-to-end Analysis of Sequence Trees - MSGM: Multi-species genome models - MM: Morphological models - MODELSELECTION: Model selection tools - MSBD: Multi-species birth-death - ORC: Optimized relaxed clock - SA: Sampled ancestors - speedemon: Speed monitoring tools - SSM: Structured skyline models - STACEY: Species tree and classification estimation - StarBEAST2: Species tree analysis - starbeast3: Enhanced species tree analysis - TreeStat2: Tree statistics