beast-mcmc - Online in the Cloud

PROGRAM:

NAME

beast-mcmc - Bayesian evolutionary analysis sampling trees

SYNOPSIS

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 |
input.xml]

DESCRIPTION

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).

OPTIONS

-verbose
verbose XML parsing messages

-strict
fail on non conforming BEAST XML file

-window
provide a console window

-options
display an options dialog

-working
change working directory to input file´s directory

-seed
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)

-java
use Java only, no native implementations

-beagle
use beagle library if available

-beagle_info
show information on available beagle resources

-beagle_resource_order
set order of beagle resources

-help
print usage screen

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