title: CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.
abstract: 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.
authors.affiliation: 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.
authors.forename: Miguel
authors.initials: M
authors.lastname: Arenas
authors.affiliation: Instituto Gulbenkian de Ciencia, Oeiras, Portugal.
authors.forename: Joao S
authors.initials: JS
authors.lastname: Lopes
authors.affiliation: School of Mathematical Sciences and School of Biological Sciences, University of Bristol, University Walk, Bristol, United Kingdom.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Beaumont
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Posada
mesh_terms: D001499:Bayes Theorem; D003198:Computer Simulation; D016013:Likelihood Functions; D059645:Mutation Rate; D016366:Open Reading Frames / Q000235:genetics*; D011995:Recombination, Genetic; D012984:Software
keywords: approximate Bayesian computation; coding data; molecular adaptation; recombination; substitution rate