ArticlePloS one2012
Developing and applying heterogeneous phylogenetic models with XRate.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Physical and Functional Analysis of Viral RNA Genomes by SHAPE.Annual review of virology · 2019Review
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
- AAV ancestral reconstruction library enables selection of broadly infectious viral variants.Gene therapy · 2015Article
- Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity.Journal of virology · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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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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