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Developing and Applying Heterogeneous Phylogenetic Models with XRate

Authors
Journal
PLoS ONE
1932-6203
Publisher
Public Library of Science
Publication Date
Volume
7
Issue
6
Identifiers
DOI: 10.1371/journal.pone.0036898
Keywords
  • Research Article
  • Biology
  • Computational Biology
  • Evolutionary Biology
  • Evolutionary Processes
  • Mutation
  • Evolutionary Systematics
  • Phylogenetics
  • Comparative Genomics
  • Evolutionary Genetics
  • Genomic Evolution
  • Genomics
  • Genome Analysis Tools
  • Gene Prediction
  • Genome Scans
  • Genome Evolution
  • Computer Science
  • Computer Modeling
  • Computing Methods
  • Mathematical Computing
  • Numerical Analysis
Disciplines
  • Biology
  • Computer Science

Abstract

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the “grammar” of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate 's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate 's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART.

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