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
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 http://code.google.com/p/beast-mcmc/issues/list.
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.
COPYRIGHT
Copyright © 2002-2010 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST)Copyright © 2009-2010 Felix Feyertag (This manpage)
The binaries and source code are made available and can be distributed subject to the following conditions:
BEAST is Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License. See the notice in individual files and the file LICENSE for licensing details.
BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses.
- •This product includes software developed by the JDOM Project (http://www.jdom.org/)
- •This product includes software developed by The Apache Software Foundation (http://www.apache.org/)
- •The license for JDOM can be read in the LICENSE.txt file in the source distribution available at http://www.jdom.org/
- •The license for the Commons Math library can be read at http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE.txt file in the source distribution available at http://jakarta.apache.org/commons/math/
This manual page and its XML source can be used, modified, and redistributed as if it were in public domain.