Reference EntryDOI
PHYLIP (Phylogeny Inference Package)
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This article is published in Dictionary of Bioinformatics and Computational Biology.The article was published on 2004-10-15. It has received 4301 citations till now. The article focuses on the topics: Inference.read more
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
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MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
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jModelTest: Phylogenetic Model Averaging
TL;DR: jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" that implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion", the "Bayesian information criterion," and a "decision-theoretic performance-based" approach.
Journal ArticleDOI
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
Todd Z. DeSantis,Philip Hugenholtz,Neils Larsen,Mark Rojas,Eoin L. Brodie,Keith Keller,Thomas Huber,Daniel Dalevi,Ping Hu,Gary L. Andersen +9 more
TL;DR: A 16S rRNA gene database (http://greengenes.lbl.gov) was used to provide chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies as mentioned in this paper.
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Application of Phylogenetic Networks in Evolutionary Studies
Daniel H. Huson,David Bryant +1 more
TL;DR: This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted and outlines the beginnings of a comprehensive statistical framework for applying split network methods.
References
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Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Journal ArticleDOI
Evolutionary trees from DNA sequences: A maximum likelihood approach
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Related Papers (5)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more