Developing and Applying Heterogeneous Phylogenetic Models with XRate

PLoS One

Oscar Westesson¹ 

[1] Department of Bioengineering, University of California, Berkeley, California, United States of America

关键词: Grammar;    Sequence alignment;    Phylogenetic analysis;    Multiple alignment calculation;    Phylogenetics;    Syntax;    RNA structure;    Language;   

DOI  :  10.1371/journal.pone.0036898

学科分类：医学（综合）

来源: Public Library of Science

【 摘 要 】

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.

【 授权许可】

CC BY