BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Manual

Bayesian Analysis to Describe Genomic Evolution by Rearrangement (BADGER) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing genome arrangements including mitochondrial DNA The main program uses a variety of Metropolis-Hastings proposal mechanisms to sample from the joint posterior distribution of phylogenetic trees using a model of evolution by reversals of the genomic arrangement. Other programs in the distribution help in analysis of the sampled trees and clades.

The free software is available from the BADGER homepage.

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

Simon, D. and B. Larget. 2004. Bayesian Analysis to Describe Genomic Evolution by Rearrangement (BADGER), version 1.02 beta. Department of Mathematics and Computer Science, Duquesne University.

Donald Simon
Department of Mathematics and Computer Science
Duquesne University
Pittsburgh, PA 15282
Phone: (412) 396-6467
FAX: (412) 396-5197
E-mail: simon@mathcs.duq.edu

Bret Larget
Department of Botany
University of Wisconsin
430 Lincoln Dr.
Madison, WI 53706
Phone: (608) 265-6799 (Botany), (608) 262-7979 (Statistics)
E-mail: brlarget@wisc.edu

E-mail: badger@badger.duq.edu
Web: http://www.badger.duq.edu

Table of Contents

• Legal agreement
• Changes in this version
• Obtaining the software
• Files in the distribution
• Installing the software
• Running the programs
• Run control file format
  • Table of run control file options
• Generating multiple run control files
• Input files
• Output files
• Groups
• Models
• Summarizing output files
• Comparing common clade lists
• MCMC algorithms
  • Tree representation
  • Tree proposal algorithms
  • Finding new reversal lists
  • Algorithms when grouping is used
  • Selecting Algorithms
• MCMC convergence
• An example
• Glossary
• Acknowledgments
• References

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