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MrBayes 3.2.2 on XSEDE

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes' theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

MrBayes 3.2.2 on XSEDE provides a primitive interface that submits jobs to Gordon, a large NSF XSEDE Resource. The interface currently supports submissions for jobs that are configured via a MrBayes Block in the NEXUs input file. If you need the ability to configure job runs via the interface, as with the MrBayes 3.1.2 interface, please contact us and let us know.

MrBayes 3.2.2 provides new features. It supports commands for BEST (Bayesian Estimation of Species Trees). It also supports checkpointing, which makes it possible to restart a run that has terminated unexpectedly, or that has reached the end of the maximum allowed run time without converging. While MrBayes 3.2.2 code supports the use of GPUs via BEAGLE, we do not currently support that option. Nevetheless, the new code offers signficant speed ups on XSEDE.

Manual for MrBayes 3.2.2: http://mrbayes.sourceforge.net/mb3.2_manual.pdf

MrBayes mail list: http://sourceforge.net/mailarchive/forum.php?forum=mrbayes-users

MRBAYES home page here.

INPUT = dna or protein matrices in Nexus format

Simple Example of Run Input/Output

Input File Type	File Name
input file	infile.nex
example MB block	mbblock.nex
Output File Type	File Name
log file	log.txt and mrbayeslog.out
sump_output	infile.nex.run1.p
	infile.nex.run2.p
	sumpoutput.out
sumt_output	infile.nex.run1.t
	infile.nex.run2.t
all_mcmc_trees	infile.nex.trprobs
partition information	infile.nex.parts
consensus_tree	infile.nex.con
acceptance_ratios	infile.nex.mcmc

Known Issues:

• MrBayes 3.2.2 run with BEAGLE fails quickly with a few data sets. The cuase is presently unknown, but you can uncheck the Run Using Beagle box, and these runs will always succeed.
• A few datasets/configurations hang with MB 3.2.2, but these few jobs have always run fine with MB 3.1.2.

If there is a tool or a feature you need, please let us know.