A python extension for phylogenetic analysis. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used Harmonic Mean estimator. Phycas provides for analyses in which the prior on tree topologies allows polytomous trees as well as fully resolved trees, and provides for several choices for edge length priors, including a hierarchical model as well as the recently described compound Dirichlet prior, which helps avoid overly informative induced priors on tree length.

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Phycas classification

Phycas specifications

Software type:
Package
Restrictions to use:
None
Output data:
Phylogenetic trees
Operating system:
Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://hydrodictyon.eeb.uconn.edu/projects/phycas/downloads/v2.2/phycas-2.2.0-win.zip
Interface:
Command line interface
Input data:
Nucleotide sequence data
Output format:
NEXUS
Programming languages:
C++, Python
Version:
2.2.0
Requirements:
Python v. 2.7+

Publications

  • (Lewis et al., 2015) Phycas: Software for Bayesian Phylogenetic Analysis. Systematic Biology.
    PMID: 25577605

Phycas support

Documentation

Maintainer

Credits

Institution(s)

Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA; Department of Ecology and Evolution, University of Kansas, Lawrence, KS, USA; Department of Biology, Duke University, Durham, NC, USA

Funding source(s)

This project was supported by the National Science Foundation (grants No. EF-0331495, No. DEB-1036448, and No.DEB-1354146) and the Alfred P. Sloan Foundation (grant No. 98-4-5 ME), the National Science Foundation grant No. DEB-0732920, the National Evolutionary Synthesis Center, the National Science Foundation grant No. EF-0423641 and the Department of Ecology and Evolutionary Biology at the University of Kansas.

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