Literature DB >> 18428705

Using MODELTEST and PAUP* to select a model of nucleotide substitution.

David Posada1.   

Abstract

Models of nucleotide substitution are commonly used in the analysis of DNA sequences. This unit describes the use of the program MODELTEST (coupled with PAUP*) to find the best-fit model of substitution for the sequence alignment at hand. An example data file is analyzed and the interpretation of the results is discussed. Some background theory on model selection and a discussion of the relevance of models is included at the end of the unit.

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Year:  2003        PMID： 18428705     DOI： 10.1002/0471250953.bi0605s00

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  73 in total

1.  Supplemental description and molecular characterization of Myxobolus miyarii Kudo, 1919 (Myxosporea: Myxobolidae) infecting intestine of Amur catfish (Silurus asotus).

Authors:  X H Liu; J Y Zhang; M D Batueva; V N Voronin
Journal:  Parasitol Res       Date:  2015-12-21       Impact factor: 2.289

2.  Molecular evolution of the Helicobacter pylori vacuolating toxin gene vacA.

Authors:  Kelly A Gangwer; Carrie L Shaffer; Sebastian Suerbaum; D Borden Lacy; Timothy L Cover; Seth R Bordenstein
Journal:  J Bacteriol       Date:  2010-09-24       Impact factor: 3.490

3.  GATA transcription factors in vertebrates: evolutionary, structural and functional interplay.

Authors:  Yanyan Tang; Yunfei Wei; Wenwu He; Yongbo Wang; Jianing Zhong; Chao Qin
Journal:  Mol Genet Genomics       Date:  2013-12-25       Impact factor: 3.291

4.  Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing.

Authors:  Marion Fischer-Le Saux; Sophie Bonneau; Salwa Essakhi; Charles Manceau; Marie-Agnès Jacques
Journal:  Appl Environ Microbiol       Date:  2015-05-01       Impact factor: 4.792

5.  Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008.

Authors:  Sheng-Wen Huang; Yun-Wei Hsu; Derek J Smith; David Kiang; Huey-Pin Tsai; Kuei-Hsiang Lin; Shih-Min Wang; Ching-Chung Liu; Ih-Jen Su; Jen-Ren Wang
Journal:  J Clin Microbiol       Date:  2009-09-23       Impact factor: 5.948

6.  New insights into the evolution and functional divergence of the SWEET family in Saccharum based on comparative genomics.

Authors:  Weichang Hu; Xiuting Hua; Qing Zhang; Jianping Wang; Qiaochu Shen; Xingtan Zhang; Kai Wang; Qingyi Yu; Yann-Rong Lin; Ray Ming; Jisen Zhang
Journal:  BMC Plant Biol       Date:  2018-11-07       Impact factor: 4.215

7.  Vertebrate paralogous CRMPs in nervous system: evolutionary, structural, and functional interplay.

Authors:  Yanyan Tang; Ziming Ye; Yunfei Wei; Cuiting Lin; Yongbo Wang; Chao Qin
Journal:  J Mol Neurosci       Date:  2014-06-05       Impact factor: 3.444

8.  J-Western forms of Helicobacter pylori cagA constitute a distinct phylogenetic group with a widespread geographic distribution.

Authors:  Stacy S Duncan; Pieter L Valk; Carrie L Shaffer; Seth R Bordenstein; Timothy L Cover
Journal:  J Bacteriol       Date:  2012-01-13       Impact factor: 3.490

9.  A revised timescale for human evolution based on ancient mitochondrial genomes.

Authors:  Qiaomei Fu; Alissa Mittnik; Philip L F Johnson; Kirsten Bos; Martina Lari; Ruth Bollongino; Chengkai Sun; Liane Giemsch; Ralf Schmitz; Joachim Burger; Anna Maria Ronchitelli; Fabio Martini; Renata G Cremonesi; Jiří Svoboda; Peter Bauer; David Caramelli; Sergi Castellano; David Reich; Svante Pääbo; Johannes Krause
Journal:  Curr Biol       Date:  2013-03-21       Impact factor: 10.834

10.  Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus.

Authors:  Rubing Chen; Vinita Puri; Nadia Fedorova; David Lin; Kumar L Hari; Ravi Jain; Juan David Rodas; Suman R Das; Reed S Shabman; Scott C Weaver
Journal:  J Virol       Date:  2016-11-14       Impact factor: 5.103
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