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
BUGS
The BEAST bug tracking system can be found at https://github.com/beast-dev/beast-mcmc/issues.
SEE ALSO
REFERENCES
• Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214.
• Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.
• Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.
• Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.
AUTHORS
Alexei J. Drummond
-
Copyright holder for BEAST.
Andrew Rambaut
-
Copyright holder for BEAST.
Marc A. Suchard
-
Copyright holder for BEAST.
Felix Feyertag <[email protected]>
-
Prepared this manpage in DocBook XML for the Debian distribution.