MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
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The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.Abstract:
Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.read more
Citations
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HyPhy: hypothesis testing using phylogenies
TL;DR: The HyPhypackage is designed to provide a flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.
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Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
TL;DR: This study illustrates how combining comparative metagenomics with gnotobiotic mouse models and specific dietary manipulations can disclose the niches of previously uncharacterized members of the gut microbiota.
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Ultrafast Approximation for Phylogenetic Bootstrap
TL;DR: This work proposes an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees and offers an efficient and easy-to-use software to perform the UFBoot analysis with ML tree inference.
Journal ArticleDOI
Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans
Rebecca Garten,C. Todd Davis,Colin A. Russell,Colin A. Russell,Bo Shu,Stephen Lindstrom,Amanda Balish,Wendy Sessions,Xiyan Xu,Eugene Skepner,Varough M. Deyde,Margaret Okomo-Adhiambo,Larisa V. Gubareva,John R. Barnes,Catherine B. Smith,Shannon L. Emery,Michael J. Hillman,Pierre Rivailler,James A. Smagala,Miranda de Graaf,Miranda de Graaf,David F. Burke,Ron A. M. Fouchier,Claudia Pappas,Celia Alpuche-Aranda,Hugo López-Gatell,Hiram Olivera,Irma Lopez,Christopher A. Myers,Dennis J. Faix,Patrick J. Blair,Cindy Yu,Kimberly M. Keene,P. David Dotson,David Boxrud,Anthony R. Sambol,Syed H. Abid,Kirsten St. George,Tammy L. Bannerman,Amanda L. Moore,David J. Stringer,Patricia Blevins,Gail J. Demmler-Harrison,Michele Ginsberg,Paula Kriner,Steve Waterman,Sandra Smole,Hugo Guevara,Edward A. Belongia,Patricia A. Clark,Sara T. Beatrice,Ruben O. Donis,Jacqueline M. Katz,Lyn Finelli,Carolyn B. Bridges,Michael W. Shaw,Daniel B. Jernigan,Timothy M. Uyeki,Derek J. Smith,Derek J. Smith,Derek J. Smith,Alexander Klimov,Nancy J. Cox +62 more
TL;DR: The lack of similarity between the 2009 A(H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period as mentioned in this paper.
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Approximate likelihood-ratio test for branches : A fast, accurate, and powerful alternative
Maria Anisimova,Olivier Gascuel +1 more
TL;DR: A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support and is shown to be accurate, powerful, and robust to certain violations of model assumptions.
References
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