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A Bayesian Markov chain Monte Carlo (MCMC) program for analyzing DNA sequence alignments under the multispecies coalescent model (MSC). BPP analyses may include estimation of population size (theta's) and species divergence times (tau's), species tree estimation and species delimitation. BPP replaces the old program MCMCcoal.

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BPP versioning

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BPP classification

BPP specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
PHYLIP/PAML
Output format:
TXT
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
A control file, a sequence alignment file, an Imap file
Output data:
Summary
Operating system:
Unix/Linux, Mac OS, Windows
Version:
3.3
Source code URL:
http://abacus.gene.ucl.ac.uk/software/bpp3.3.tgz

BPP support

Maintainer

  • Ziheng Yang <>

Credits

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Publications

Institution(s)

Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, UK

Funding source(s)

This study is supported by a grant from the Biotechnological and Biological Sciences Research Council (BBSRC).

Link to literature

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