Developing and applying heterogeneous phylogenetic models with XRate.

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 m...

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Autores principales:	Oscar Westesson, Ian Holmes
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/634fb29efaae43498811ce2a550ecb90
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spelling	oai:doaj.org-article:634fb29efaae43498811ce2a550ecb902021-11-18T07:16:19ZDeveloping and applying heterogeneous phylogenetic models with XRate.1932-620310.1371/journal.pone.0036898https://doaj.org/article/634fb29efaae43498811ce2a550ecb902012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22693624/?tool=EBIhttps://doaj.org/toc/1932-6203Modeling 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.Oscar WestessonIan HolmesPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 6, p e36898 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Oscar Westesson Ian Holmes Developing and applying heterogeneous phylogenetic models with XRate.
description	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.
format	article
author	Oscar Westesson Ian Holmes
author_facet	Oscar Westesson Ian Holmes
author_sort	Oscar Westesson
title	Developing and applying heterogeneous phylogenetic models with XRate.
title_short	Developing and applying heterogeneous phylogenetic models with XRate.
title_full	Developing and applying heterogeneous phylogenetic models with XRate.
title_fullStr	Developing and applying heterogeneous phylogenetic models with XRate.
title_full_unstemmed	Developing and applying heterogeneous phylogenetic models with XRate.
title_sort	developing and applying heterogeneous phylogenetic models with xrate.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/634fb29efaae43498811ce2a550ecb90
work_keys_str_mv	AT oscarwestesson developingandapplyingheterogeneousphylogeneticmodelswithxrate AT ianholmes developingandapplyingheterogeneousphylogeneticmodelswithxrate
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Developing and applying heterogeneous phylogenetic models with XRate.

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