Developing and applying heterogeneous phylogenetic models with XRate

Details Developing and applying heterogeneous phylogenetic models with XRate Developing and applying heterogeneous phylogenetic models with XRate

2012-02-17

arxiv.org/abs/1202.3834v1

Biology

Quantitative Biology

Quantitative Methods

34 pages, 3 figures, glossary of XRate model terminology

Scientific paper

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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