beast-mcmc1
Bayesian evolutionary analysis sampling trees
Usage
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}]
Overview
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
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.
Releases
6 releases since Debian 8 (Jessie); the text changed 1 time.