ArticleBioinformatics (Oxford, England)2014
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
- Article
- Separating selection from mutation in antibody language models.bioRxiv : the preprint server for biology · 2025Article
- Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.Journal of molecular evolution · 2025Article
- Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination.Molecular biology and evolution · 2024Article
- Rediscovering the unusual, solitary bryozoan Monobryozoon ambulans Remane, 1936: first molecular and new morphological data clarify its phylogenetic position.Frontiers in zoology · 2024Article
- The hagfish genome and the evolution of vertebrates.Nature · 2024Article
- Article
- Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family.BMC biology · 2022Article
- Host Adaptation in Legionellales Is 1.9 Ga, Coincident with Eukaryogenesis.Molecular biology and evolution · 2022Article
- Bioinformatics for the Origin and Evolution of Viruses.Advances in experimental medicine and biology · 2022Article
- Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications.Frontiers in genetics · 2022Article
- Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage.Genome biology and evolution · 2021Article
- Inferring Long-Term Effective Population Size with Mutation-Selection Models.Molecular biology and evolution · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- A Bayesian Mutation-Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes.Molecular biology and evolution · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- The origin and diversification of pteropods precede past perturbations in the Earth's carbon cycle.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.Molecular biology and evolution · 2019Article
- Population and Culture Age Influence the Microbiome Profiles of House Dust Mites.Microbial ecology · 2019Article
- Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.Molecular biology and evolution · 2019Article
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2 authors.
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Abstract
motivationIn 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 oversimplified assumptions, questionable statistical methods or a limited focus on small data sets.
resultsHere, 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 AND IMPLEMENTATION: The models are implemented within the PhyloBayes-MPI package, (available at phylobayes.org) along with usage details in the accompanying manual.
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