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CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.
Arenas, Miguel; Lopes, Joao S; Beaumont, Mark A; Posada, David.
Afiliación
  • Arenas M; Centre for Molecular Biology "Severo Ochoa," Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain marenas@cbm.csic.es.
  • Lopes JS; Instituto Gulbenkian de Ciencia, Oeiras, Portugal.
  • Beaumont MA; School of Mathematical Sciences and School of Biological Sciences, University of Bristol, University Walk, Bristol, United Kingdom.
  • Posada D; Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain.
Mol Biol Evol ; 32(4): 1109-12, 2015 Apr.
Article en En | MEDLINE | ID: mdl-25577191
The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Recombinación Genética / Simulación por Computador / Sistemas de Lectura Abierta / Tasa de Mutación Tipo de estudio: Prognostic_studies Idioma: En Revista: Mol Biol Evol Asunto de la revista: BIOLOGIA MOLECULAR Año: 2015 Tipo del documento: Article País de afiliación: España Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Recombinación Genética / Simulación por Computador / Sistemas de Lectura Abierta / Tasa de Mutación Tipo de estudio: Prognostic_studies Idioma: En Revista: Mol Biol Evol Asunto de la revista: BIOLOGIA MOLECULAR Año: 2015 Tipo del documento: Article País de afiliación: España Pais de publicación: Estados Unidos