PLoS One | |
Developing and Applying Heterogeneous Phylogenetic Models with XRate | |
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
【 预 览 】
Files | Size | Format | View |
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RO201901226629124ZK.pdf | 286KB | download |