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Phycas: software for Bayesian phylogenetic analysis.

Paul O Lewis1, Mark T Holder2, David L Swofford2

  • 1Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA; Department of Ecology and Evolution, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA; and Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA paul.lewis@uconn.edu.

Systematic Biology
|January 12, 2015
PubMed
Summary
This summary is machine-generated.

Phycas is a free, open-source Bayesian phylogenetics software. It enhances model selection for nucleotide sequences using advanced methods for marginal likelihood estimation and offers flexible prior options for tree topologies and edge lengths.

Keywords:
Bayes FactorBayesian phylogeneticsconditional predictive ordinatesdata partitioningmarginal likelihoodposterior predictive model selectionsteppingstone method

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Bayesian phylogenetics is crucial for inferring evolutionary relationships.
  • Accurate model selection is essential for robust phylogenetic inference.
  • Existing software may have limitations in model selection accuracy and flexibility.

Purpose of the Study:

  • Introduce Phycas, a new open-source Bayesian phylogenetics software.
  • Provide advanced methods for Bayesian model selection in phylogenetics.
  • Enhance the accuracy and flexibility of phylogenetic analyses.

Main Methods:

  • Phycas utilizes C++ with a Python interface for broad accessibility.
  • Implements advanced marginal likelihood estimation techniques like Thermodynamic Integration and Generalized Steppingstone.
  • Supports posterior predictive model selection methods (Gelfand-Ghosh, Conditional Predictive Ordinates).

Main Results:

  • Phycas offers more accurate marginal likelihood estimation than traditional methods.
  • The software supports a variety of substitution models (GTR, codon) and data partitioning.
  • Phycas allows flexible priors on tree topologies and edge lengths, including novel options.

Conclusions:

  • Phycas provides a powerful and flexible tool for Bayesian phylogenetics.
  • Its advanced model selection capabilities improve the reliability of evolutionary inference.
  • The software's open-source nature and comprehensive features benefit the research community.