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Bioinformatics. 2013 Dec 18. [Epub ahead of print]
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
Rodrigue N, Lartillot N.
Author information
Abstract
MOTIVATION:
In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of over-simplified assumptions, questionable statistical methods, or a limited focus on small data sets.
RESULTS:
Here, we offer a scalable, message-passing-interface-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree, and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.
AVAILABILITY:
The models are implemented within the PhyloBayes-MPI package, available on our website (phylobayes.org) along with usage details in the accompanying manual.
CONTACT:
nicolas.rodrigue@ucalgary.ca.
PMID:
24351710
[PubMed - as supplied by publisher]
Free full text
Bioinformatics. 2013 Dec 18. [Epub ahead of print]
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
Rodrigue N, Lartillot N.
Author information
Abstract
MOTIVATION:
In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of over-simplified assumptions, questionable statistical methods, or a limited focus on small data sets.
RESULTS:
Here, we offer a scalable, message-passing-interface-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree, and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.
AVAILABILITY:
The models are implemented within the PhyloBayes-MPI package, available on our website (phylobayes.org) along with usage details in the accompanying manual.
CONTACT:
nicolas.rodrigue@ucalgary.ca.
PMID:
24351710
[PubMed - as supplied by publisher]
Free full text
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
Rodrigue N, Lartillot N.
Author information
Abstract
MOTIVATION:
In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of over-simplified assumptions, questionable statistical methods, or a limited focus on small data sets.
RESULTS:
Here, we offer a scalable, message-passing-interface-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree, and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.
AVAILABILITY:
The models are implemented within the PhyloBayes-MPI package, available on our website (phylobayes.org) along with usage details in the accompanying manual.
CONTACT:
nicolas.rodrigue@ucalgary.ca.
PMID:
24351710
[PubMed - as supplied by publisher]
Free full text
Bioinformatics. 2013 Dec 18. [Epub ahead of print]
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
Rodrigue N, Lartillot N.
Author information
Abstract
MOTIVATION:
In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational demands of these models have sometimes lead to the adoption of over-simplified assumptions, questionable statistical methods, or a limited focus on small data sets.
RESULTS:
Here, we offer a scalable, message-passing-interface-based Bayesian implementation of site-heterogeneous codon models in the mutation-selection framework. Our software jointly infers the global mutational parameters at the nucleotide level, the branch lengths of the tree, and a Dirichlet process governing across-site variation at the amino acid level. We focus on an example estimation of the distribution of selection coefficients from an alignment of several hundred sequences of the influenza PB2 gene, and highlight the site-specific characterization enabled by such a modeling approach. Finally, we discuss future potential applications of the software for conducting evolutionary inferences.
AVAILABILITY:
The models are implemented within the PhyloBayes-MPI package, available on our website (phylobayes.org) along with usage details in the accompanying manual.
CONTACT:
nicolas.rodrigue@ucalgary.ca.
PMID:
24351710
[PubMed - as supplied by publisher]
Free full text