Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

Bioinformatics
Nicolas Rodrigue, Nicolas Lartillot

Abstract

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 oversimplified assumptions, questionable statistical methods or a limited focus on small data sets. 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. The models are implemented within the PhyloBayes-MPI package, (available at phylobayes.org) along with usage details in the accompanying manual.

References

Jul 10, 1998·Molecular Biology and Evolution·A L Halpern, W J Bruno
Jan 8, 2008·Molecular Biology and Evolution·Ziheng Yang, Rasmus Nielsen
Sep 29, 2009·Molecular Biology and Evolution·A P Jason de KoningDavid D Pollock
Feb 24, 2010·Proceedings of the National Academy of Sciences of the United States of America·Nicolas RodrigueNicolas Lartillot
Sep 15, 2012·Molecular Biology and Evolution·Austin G Meyer, Claus O Wilke
Feb 26, 2013·Molecular Biology and Evolution·Manuel GilMaria Anisimova

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Citations

Aug 19, 2015·BMC Evolutionary Biology·Nicolas StraubeGavin J P Naylor
Jan 13, 2015·Molecular Biology and Evolution·Stephanie J Spielman, Claus O Wilke
Sep 24, 2015·PloS One·Stephanie J Spielman, Claus O Wilke
Apr 22, 2014·Molecular Phylogenetics and Evolution·Gregg P RobideauC André Lévesque
Aug 12, 2016·Molecular Biology and Evolution·Stephanie J Spielman, Claus O Wilke
Mar 30, 2018·Molecular Biology and Evolution·Christopher T JonesJoseph P Bielawski
Mar 2, 2018·F1000Research·Dariya K SydykovaClaus O Wilke
Dec 12, 2018·Genome Biology and Evolution·Francisco Figueroa-MartinezAdrian Reyes-Prieto
Mar 25, 2019·Molecular Biology and Evolution·Karen Siu-TingChristopher J Creevey
Nov 23, 2018·Microbial Ecology·Jan HubertPavel Klimov
Feb 28, 2019·BMC Evolutionary Biology·S Omar Kazmi, Nicolas Rodrigue
Sep 9, 2020·Molecular Biology and Evolution·Noor YoussefJoseph P Bielawski
Aug 12, 2016·Molecular Biology and Evolution·Romain DerelleDavid Moreira
Jan 24, 2018·Genome Biology and Evolution·Matthew W BrownAndrew J Roger
Sep 26, 2020·Proceedings of the National Academy of Sciences of the United States of America·Katja T C A PeijnenburgFerdinand Marlétaz
Jan 4, 2020·Development·José M Martín-Durán, Ferdinand Marlétaz
Nov 25, 2020·Journal of Molecular Evolution·Mackenzie M Johnson, Claus O Wilke
Oct 13, 2020·Molecular Biology and Evolution·Nicolas RodrigueNicolas Lartillot
Jan 15, 2019·Current Biology : CB·Ferdinand MarlétazDaniel S Rokhsar
Jan 23, 2021·Briefings in Bioinformatics·Roberto Del AmparoMiguel Arenas
Jul 1, 2021·Molecular Biology and Evolution·Thibault LatrilleNicolas Lartillot
Sep 29, 2021·Genome Biology and Evolution·Tristan L Stark, David A Liberles

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Software Mentioned

PhyloBayes
MPI

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