BAMBE Bayesian Analysis in Molecular Biology and Evolution
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BAMBE Tags

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BAMBE Description

The name BAMBE stands for Bayesian Analysis in Molecular Biology and Evolution. BAMBE was developed to be a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing aligned DNA or RNA sequence data and allows data sets with gaps or indeterminate sites. The main program uses a variety of Metropolis-Hastings algorithms to sample from the joint posterior distribution of phylogenetic trees and likelihood model parameters. Other programs in the distribution help in analysis of the sampled trees and parameter values. NOTE: Everyone is granted permission to copy and use this software package and the accompanying documentation for personal academic use Main features: A choice of likelihood models. HKY85 (Hasegawa-Kishino-Yano, 1985) F84 (as implemented in Felsenstein's PHYLIP) TN93 (Tamura-Nei, 1993) A choice of Metropolis-Hastings samplers for proposing new phylogenetic trees (including a new scaled Beta distribution version of local). Metropolis-Hastings samplers for proposing new model parameters. The choice of separate samplers for burn-in and inference. Flexible specification of site categories with separate parameter values for each site category. A choice to initialize the search at a random tree, the UPGMA tree, the Neighbor-joining tree, or a user-defined tree. Two formats (BAMBE and Newick) for reading and writing trees. HTML Help files. Graphical real-time monitoring of the tree and model parameters.

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