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MrBayes

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.

Manual: http://mrbayes.csit.fsu.edu/wiki/index.php/Manual

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

 

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