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MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA. Key words evolution genomics software data mining sequence alignment distance phylogenetics selection © Henry Stewart Publications « Previous | Next Article » Table of Contents This Article Brief Bioinform (2004) 5 (2): 150-163. doi: 10.1093/bib/5.2.150 » Abstract Free Full Text (PDF) Free Classifications Paper Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Kumar, S. Articles by Nei, M. Search for related content PubMed PubMed citation Articles by Kumar, S. Articles by Tamura, K. Articles by Nei, M. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue September 2015 16 (5) Alert me to new issues The Journal About the Journal Rights & Permissions Publishers' Books for Review Dispatch date of the next issue We are mobile – find out more This journal is a member of the Committee on Publication Ethics (COPE) Journals Career Network Impact Factor: 9.617 5-Yr impact factor: 7.017 Managing Editor Martin Bishop View full editorial board For Authors Services for authors Instructions to authors Online submission Submit now Author Self Archiving Policy Open Access options for authors - visit OxfordOpen This journal enables compliance with the NIH Public Access Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services What we offer Advertising sales Reprints Supplements Widget Get a widget var taxonomies = ("SCI01060"); Most Most Read A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis A survey of tools for variant analysis of next-generation genome sequencing data Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline Comparison of software packages for detecting differential expression in RNA-seq studies Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration » View all Most Read articles Most Cited MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Recent developments in the MAFFT multiple sequence alignment program MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration PROSITE: A documented database using patterns and profiles as motif descriptors » View all Most Cited articles Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department. Online ISSN 1477-4054 - Print ISSN 1467-5463 Copyright © 2015 Oxford University Press Oxford Journals Oxford University Press Site Map Privacy Policy Cookie Policy Legal Notices Frequently Asked Questions Other Oxford University Press sites: Oxford University Press Oxford Journals China Oxford Journals Japan Academic & Professional books Children's & Schools Books Dictionaries & Reference Dictionary of National Biography Digital Reference English Language Teaching Higher Education Textbooks International Education Unit Law Medicine Music Online Products & Publishing Oxford Bibliographies Online Oxford Dictionaries Online Oxford English Dictionary Oxford Language Dictionaries Online Oxford Scholarship Online Reference Rights and Permissions Resources for Retailers & Wholesalers Resources for the Healthcare Industry Very Short Introductions World's Classics function fnc_onDomLoaded() { var query_context = getQueryContext(); PF_initOIUnderbar(query_context,":QS:default","","JRN"); PF_insertOIUnderbar(0); }; if (window.addEventListener) { window.addEventListener('load', fnc_onDomLoaded, false); } else if (window.attachEvent) { window.attachEvent('onload', fnc_onDomLoaded); } var gaJsHost = (("https:" == document.location.protocol) ? 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MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

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Publisher
Oxford University Press
Copyright
Copyright © 2015 Oxford University Press
ISSN
1467-5463
eISSN
1477-4054
DOI
10.1093/bib/5.2.150
Publisher site
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Abstract

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA. Key words evolution genomics software data mining sequence alignment distance phylogenetics selection © Henry Stewart Publications « Previous | Next Article » Table of Contents This Article Brief Bioinform (2004) 5 (2): 150-163. doi: 10.1093/bib/5.2.150 » Abstract Free Full Text (PDF) Free Classifications Paper Services Article metrics Alert me when cited Alert me if corrected Find similar articles Similar articles in Web of Science Similar articles in PubMed Add to my archive Download citation Request Permissions Citing Articles Load citing article information Citing articles via CrossRef Citing articles via Scopus Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Kumar, S. Articles by Nei, M. Search for related content PubMed PubMed citation Articles by Kumar, S. Articles by Tamura, K. Articles by Nei, M. Related Content Load related web page information Share Email this article CiteULike Delicious Facebook Google+ Mendeley Twitter What's this? Search this journal: Advanced » Current Issue September 2015 16 (5) Alert me to new issues The Journal About the Journal Rights & Permissions Publishers' Books for Review Dispatch date of the next issue We are mobile – find out more This journal is a member of the Committee on Publication Ethics (COPE) Journals Career Network Impact Factor: 9.617 5-Yr impact factor: 7.017 Managing Editor Martin Bishop View full editorial board For Authors Services for authors Instructions to authors Online submission Submit now Author Self Archiving Policy Open Access options for authors - visit OxfordOpen This journal enables compliance with the NIH Public Access Policy Alerting Services Email table of contents Email Advance Access CiteTrack XML RSS feed Corporate Services What we offer Advertising sales Reprints Supplements Widget Get a widget var taxonomies = ("SCI01060"); Most Most Read A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis A survey of tools for variant analysis of next-generation genome sequencing data Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline Comparison of software packages for detecting differential expression in RNA-seq studies Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration » View all Most Read articles Most Cited MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Recent developments in the MAFFT multiple sequence alignment program MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration PROSITE: A documented database using patterns and profiles as motif descriptors » View all Most Cited articles Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department. Online ISSN 1477-4054 - Print ISSN 1467-5463 Copyright © 2015 Oxford University Press Oxford Journals Oxford University Press Site Map Privacy Policy Cookie Policy Legal Notices Frequently Asked Questions Other Oxford University Press sites: Oxford University Press Oxford Journals China Oxford Journals Japan Academic & Professional books Children's & Schools Books Dictionaries & Reference Dictionary of National Biography Digital Reference English Language Teaching Higher Education Textbooks International Education Unit Law Medicine Music Online Products & Publishing Oxford Bibliographies Online Oxford Dictionaries Online Oxford English Dictionary Oxford Language Dictionaries Online Oxford Scholarship Online Reference Rights and Permissions Resources for Retailers & Wholesalers Resources for the Healthcare Industry Very Short Introductions World's Classics function fnc_onDomLoaded() { var query_context = getQueryContext(); PF_initOIUnderbar(query_context,":QS:default","","JRN"); PF_insertOIUnderbar(0); }; if (window.addEventListener) { window.addEventListener('load', fnc_onDomLoaded, false); } else if (window.attachEvent) { window.attachEvent('onload', fnc_onDomLoaded); } var gaJsHost = (("https:" == document.location.protocol) ? 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Journal

Briefings in Bioinformatics – Oxford University Press

Published: Jun 1, 2004

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