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.The authors may be reached at:
Department of Mathematics and Computer Science
Pittsburgh, PA 15282
Phone: (412) 396-6467
FAX: (412) 396-5197
Department of Botany
University of Wisconsin
430 Lincoln Dr.
Madison, WI 53706
Phone: (608) 265-6799 (Botany), (608) 262-7979 (Statistics)
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