MrBayes is a freeware program for implementing Bayesian inference of phylogeny=
. Bayesian phylogenetic analysis proceeds by calculating the likelihood of =
the character data given an initially random tree topology, set of branch lengths and model of character ev=
olution, and iteratively modifies each of these parameters in a Markov Chai=
n Monte Carlo (MCMC) simulation. Moves that improve the likelihood of the d=
ata are always accepted, while those that do not are usually rejected (alth=
ough some may occasionally be accepted within a certain threshold so as to =
avoid getting trapped in local optima). Following an initial trial period (=
known as =E2=80=98burn in=E2=80=99), the likelihood scores will plane out a=
nd parameters will fluctuate between similar values, at which point trees a=
re sampled at regular intervals to generate a *posterior distribution of trees. Unlike the trees output by a cladistic analysis, which are bas=
ed on a single optimality criterion (**i.e.*, parsimony), the posterior distribution of trees re=
presents a set of phylogenetic hypotheses that explain the distribution of =
character states among the taxa under a range of plausible evolutionary ass=
umptions. The posterior distribution of trees can be summarised by a consen=
sus tree or =E2=80=9Cmaximum clade credibility tree=E2=80=9D, while posteri=
or probabilities for individual clades are calculated based on their freque=
ncy in the tree sample. The Bayesian approach has been found to be particul=
arly effective when there is wide variance in the amount of evolution that =
has occurred in different regions of the character data or tree, since it explic=
itly incorporates these parameters (*i.e.*, branch lengths and subst=
itution model) into the analysis.

*
*See also: =
Bayesian phylogenetics, to=
ols.

#### Reference

=E2=80=93 *MrBayes: Bayesian Inference of Phylogeny.* Computer pr=
ogram. http://mrbayes.sourceforge.net/

JT