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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Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved
Iñaki Comas,Jaidip Chakravartti,Peter M. Small,James E. Galagan,Stefan Niemann,Kristin Kremer,Joel D. Ernst,Sebastien Gagneux,Sebastien Gagneux,Sebastien Gagneux +9 more
TL;DR: A genome-wide phylogeny based on genomes of 21 strains representative of the global diversity and six major lineages of the M. tuberculosis complex showed, as expected, that essential genes in MTBC were more evolutionarily conserved than nonessential genes.
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TOPALi v2
Iain Milne,Dominik Lindner,Micha Bayer,Dirk Husmeier,Gráinne McGuire,David Marshall,Frank Wright +6 more
TL;DR: TOPALi v2 simplifies and automates the use of several methods for the evolutionary analysis of multiple sequence alignments and phylogenetic tree estimation using the Bayesian inference and maximum likelihood approaches.
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Using Phylogenetic, Functional and Trait Diversity to Understand Patterns of Plant Community Productivity
TL;DR: The results reveal that functional differences among species involve a complex suite of traits and that perhaps phylogenetic relationships provide a better measure of the diversity among species that contributes to productivity than individual or small groups of traits.
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ViPR: an open bioinformatics database and analysis resource for virology research
Brett E. Pickett,Eva L. Sadat,Yun Zhang,Jyothi M. Noronha,R. Burke Squires,Victoria Hunt,Mengya Liu,Sanjeev Kumar,Sam Zaremba,Zhiping Gu,Liwei Zhou,Christopher N. Larson,Jonathan Dietrich,Edward B. Klem,Richard H. Scheuermann +14 more
TL;DR: The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program.
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Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.
TL;DR: The phylogenetic analysis suggests that New World dwarf boas are not monophyletic, and is finds Exiliboa and Ungaliophis to be most closely related to sand boas, boas and advanced snakes, whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation.
References
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TL;DR: In this article, a new estimate minimum information theoretical criterion estimate (MAICE) is introduced for the purpose of statistical identification, which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure.
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
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