BAMBE

Bayesian Analysis in Molecular Biology and Evolution

Version 1.01 beta, October 1998

© Copyright 1998, Donald Simon & Bret Larget, Department of Mathematics and Computer Science, Duquesne University.

Bayesian Analysis in Molecular Biology and Evolution (BAMBE) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing aligned DNA or RNA sequence data and can handle gaps or indeterminate sites. The main program uses a variety of Metropolis-Hastings proposal mechanisms to sample from the joint posterior distribution of phylogenetic trees and nucleotide substitution model parameters. Other programs in the distribution help in analysis of the sampled trees and parameter values.

The free software is available from the BAMBE homepage.

If you use BAMBE to analyze data for publication, our suggested citation is:

Simon, D. and B. Larget. 1998. Bayesian analysis in molecular biology and evolution (BAMBE), version 1.01 beta. Department of Mathematics and Computer Science, Duquesne University.

Department of Mathematics and Computer Science
Duquesne University
Pittsburgh, PA 15282

Phone: (412) 396-6467
FAX: (412) 396-5197
E-mail: bambe@mathcs.duq.edu
E-mail: larget@mathcs.duq.edu
E-mail: simon@mathcs.duq.edu
Web: http://www.mathcs.duq.edu/larget/bambe.html

Table of Contents

• Legal agreement
• Obtaining the software
• Files in the distribution
• Installing the software
• Running the programs
• Sequence data format
  • Table of data symbols
• Run control file format
  • Table of run control file options
• Tree file format
• Output files
• Summarizing output files
• Likelihood models of nucleotide base substitution
• MCMC algorithms
  • GLOBAL with a molecular clock
  • GLOBAL without a molecular clock
  • LOCAL with a molecular clock
  • LOCAL without a molecular clock
  • Parameter updating
• MCMC convergence
• Glossary
• Acknowledgments
• References

Back to the table of contents.