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MrBayes 1.1

John Huelsenbeck johnh at brahms.biology.rochester.edu
Sun Jan 28 10:29:40 EST 2001


This is to announce that my program MrBayes has been
upgraded to MrBayes 1.1. The program performs Bayesian
inference of phylogeny using Markov chain Monte
Carlo. It uses a particular variant of MCMC called
Metropolis-coupled Markov chain Monte Carlo. The program
has a number of new capabilities:

  * Inference of phylogeny for amino acid data in
    addition to DNA sequence data.

  * Use of codon models for inferring positive
    selection.

  * Implements several additional models for
    accommodating among-site rate variation (equal
    rates, gamma, proportion of invariable sites,
    gamma plus proportion of invariable sites,
    site specific, site specific plus gamma,
    Yang's autocorrelated gamma rates, site specific
    plus Yang's model).

  * Improved movement across tree space.

  * Ability to summarize information on the trees
    and substitution parameters.

I have also fixed a number of annoying "features" (while
undoubtedly introducing some new ones). I have temporarily
deactivated the inference of speciation times under the
molecular clock constraint, as the routines I was using
to explore parameter space appear to do so poorly.

You can download a Macintosh executable and source code
from my WWW site at brahms.biology.rochester.edu.
Go to the software link.

John Huelsenbeck
Department of Biology
University of Rochester
Rochester, NY  14627


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