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Software

PAUP*

infers phylogenetic trees from DNA and protein sequences and morphological data according to parsimony, distance, and maximum likelihood optimality criteria. In addition to tree-searching, PAUP* provides capabilities for data-format conversion, post-tree analyses such as consensus trees and ancestral-state reconstruction, and graphical output. PAUP* executables are available to run on Macintosh, Windows, Linux and several other Unix operating systems. The most recent release of PAUP* supports multithreading on multiprocessor machines and a version under development supports parallel computation on clusters and supercomputers, using MPI or PVM to distribute tree evaluations across processors. More information is available at http://paup.scs.fsu.edu.

Migrate

is a program to estimate population sizes and asymmetrical migration rates between populations and is authored by Peter Beerli (beerli@scs.fsu.edu). Migrate uses maximum likelihood and Bayesian approaches to analyze sequences (DNA, RNA), single nucleotide polymorphisms (SNP), microsatellites, and electrophoretic markers. Both approaches utilize the Metropolis-Hastings algorithm to integrate over all possible genealogical relationships. Future developments of Migrate include; speed improvements (via code optimization and additional parallelization) and the relaxation of some population genetic assumptions (e.g., the constancy of size and migration rates through time). Migrate runs on any modern computer platform and also runs on clusters using the Message Passing Interface. The C source code is distributed free of charge from http://popgen.scs.fsu.edu/migrate.html.

MrBayes

is a program for the Bayesian estimation of phylogeny and evolution authored by John Huelsenbeck (University of California, Berkeley) and Fredrik Ronquist (Florida State University; ronquist@scs.fsu.edu). It handles a wide variety of stochastic evolutionary models for molecular, morphological and other types of discrete data. MrBayes uses Metropolis-coupled Markov chain Monte Carlo techniques to estimate the posterior probability distribution. The program runs on all common platforms and is also available in an MPI-enabled version for cluster computers and shared-memory machines. The source code and executables are distributed free of charge from http://mrbayes.net.

STMC

(STatistics and Monte Carlo) is a Fortran 77 program package authored by Bernd Berg (berg@scs.fsu.edu). It allows the user to set up Markov Chain Monte Carlo (MCMC) simulations (mainly of Statistical Physics Models) and to perform a Statistical Analysis of the generated (autocorrelated) data. Random number generators and statistics programs can be used independently from the more specific MCMC part. The program package is freely available at http://www.worldscibooks.com/physics/5602.html.