BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models.
This realisation includes all the transitions (Markov jumps) between states along phylogenetic branches and the time (Markov rewards) spent in the states between two transitions. This tutorial discusses how to estimate such quantities using stochastic mapping techniques implemented in BEAST.
BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.
About BEAST BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees. Details about the individual programs that make up the BEAST package can be found here. What does BEAST do? This is a list of some of the models and features in BEAST:
BEAST XML Elements The following is a list of valid elements in a beast file.
Custom substitution models BEAUti provides a fairly standard selection of substitution models, but BEAST can deal with a wide range of possible models through XML specification. This can be done by imposing assumptions on the general time-reversible model (GTR; Tavaré, 1986) of nucleotide substitution, or on the HKY (1985) model of nucleotide substitution. This how-to guide provides XML code ...
Tracer (now at version 1.7.2) is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. Tracer v1.7.2 can read output files from MrBayes, BEAST, BEAST2, RevBayes ...
Warning! Major spoilers ahead for Marvel's X-Men: Age of Revelation crossover event! X-Menhas confirmed the absolutely horrifying fates of Cyclops and Beast in the dark Age of Revelation future, as ...