BEAST, Bayesian Evolutionary Analysis Sampling Trees, is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. The program is orientated towards (strict and relaxed) molecular clock analyses. It can be used as a method of constructing phylogenies, but it is also intended for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. It uses an XML input format that allows the user to design and run a large range of models. We also include a graphical application that for generating this format under a wide variety of models.
- Local clock (fixed) model as option in 'Clocks' panel. Creates local rate for each taxon set with enforced monophyly.
- Multilocus models with discrete traits can be generated by BEAUti.
- Selection filters in Taxon Set panel allows quick selection by name.
- Improved robust counting under null distribution for measuring selection.
- Can link parameters in BEAUti to sample together.
- TreeAnnotator can specify burnin as number of states or trees.
- Issue 747: Robust counting with multiple partitions generates unique reference IDs in BEAUti and unique total counts for Tracer.
- Issue 743: Partitions in BEAUti should have the same number of taxa as the tree they are using.
- Issue 741: Fix negative branch length issues when sampling taxa ages from precision, or set different (default) operator.
- Issue 740: Add jitter option to continuous diffusion options in the BEAUti sites panel.
- Issue 734: BEAUti duplicates leafHeight parameters in multiple partition XMLs.
- Issue 729: Setting initial values for infinite uniform improper priors in BEAUTi.
- Issue 728: Having taxon sets defined without heights when using a user starting tree causes parsing issues.
- Issue 725: BEAUti duplicates parameter id of Markov jumps for multiple traits.
- Issue 722: Complex charsets in nexus files don't parse.
- Issue 714: sets block not recognized in 1.8.
- Issue 709: MCMC tab in Beautie v1.8.0 problem with multiple unlinked loci.