Estimating marginal likelihoods for phylogenetic models in Phycas Phycas is a software package for Bayesian phylogenetic inference (with support for ML searching planned). Paul Lewis is the primary author. Mark Holder and Dave Swofford are co-authors. Written in C++ and Python (using boost-python to create python bindings to C++ code). Compiled versions and manual: http://www.phycas.org Source: https://github.com/mtholder/Phycas
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Estimating marginal likelihoods for phylogenetic modelsin Phycas
Phycas is a software package for Bayesian phylogenetic
inference (with support for ML searching planned).
Paul Lewis is the primary author. Mark Holder and Dave
Swofford are co-authors.
Written in C++ and Python (using boost-python to create
python bindings to C++ code).
Compiled versions and manual: http://www.phycas.org
See: Xie et al. (2010); Fan et al. (2010); Lartillot
and Philippe (2006) for more discussion of estimating
marginal likelihoods.
References
Bryant, D. and Steel, M. (2009). Computing the distribution of a treemetric. IEEE IEEE/ACM Transactions on Computational Biology andBioinformatics, 6(3):420–426.
Fan, Y., Wu, R., Chen, M.-H., Kuo, L., and Lewis, P. O. (2010). Choosingamong partition models in bayesian phylogenetics. Molecular Biology andEvolution, page (advanced access).
Lartillot, N. and Philippe, H. (2006). Computing Bayes factors usingthermodynamic integration. Systematic Biology, 55(2):195–207.
Newton, M. A. and Raftery, A. E. (1994). Approximate bayesian inferencewith the weighted likelihood bootstrap. Journal of the Royal StatisticalSociety, Series B (Methodological), 56(1):3–48.
Xie, W., Lewis, P. O., Fan, Y., Kuo, L., and Chen, M.-H. (2010). Improving
marginal likelihood estimation for Bayesian phylogenetic model selection.Systematic Biology, 60(2):150–160.