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beast-mcmc - Bayesian evolutionary analysis sampling trees


beast-mcmc [OPTIONS] [input.xml]

beast-mcmc [-verbose | -strict | -window | -options | -working | -seed | -errors i |
-threads i | -java | -beagle | -beagle_info | -beagle_resource_order | -help |


BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is
orientated towards rooted, time-measured phylogenies inferred using strict or relaxed
molecular clock models. It is intended both as a method of reconstructing phylogenies and
as a framework 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. We include a simple to use user-interface
program for setting up standard analyses and a suite of programs for analysing the
results. There are three main areas of research for which the BEAUti/BEAST package is
particularly applicable. These areas are species phylogenies for molecular dating,
coalescent-based population genetics and measurably evolving populations (ancient DNA or
time-stamped viral sequence data sets).


verbose XML parsing messages

fail on non conforming BEAST XML file

provide a console window

display an options dialog

change working directory to input file´s directory

specify a random number generator seed

-errors i
maximum number of numerical errors before stopping

-threads i
the number of computational threads to use (default 1)

use Java only, no native implementations

use beagle library if available

show information on available beagle resources

set order of beagle resources

print usage screen

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