Introduction

Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. 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 newer methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used Harmonic Mean estimator. In addition, Phycas supports two posterior predictive approaches to model selection: Gelfand-Ghosh and Conditional Predictive Ordinates. The General Time Reversible family of substitution models, as well as a codon model, are available, and data can be partitioned with all parameters unlinked except tree topology and edge lengths. 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.

Publications

  1. Phycas: software for Bayesian phylogenetic analysis.
    Cite this
    Lewis PO, Holder MT, Swofford DL, 2015-05-01 - Systematic biology

Credits

  1. Paul O Lewis
    Developer

    Department of Ecology and Evolutionary Biology, University of Connecticut, United States of America

  2. Mark T Holder
    Developer

    Department of Ecology and Evolutionary Biology, University of Connecticut, United States of America

  3. David L Swofford
    Investigator

    Department of Ecology and Evolutionary Biology, University of Connecticut, United States of America

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Summary
AccessionBT000013
Tool TypeApplication
Category
Platforms
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByDavid L Swofford