A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0
Identifieur interne : 000245 ( Pmc/Checkpoint ); précédent : 000244; suivant : 000246A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0
Auteurs : Adam L. Bazinet [États-Unis] ; Derrick J. Zwickl [États-Unis] ; Michael P. Cummings [États-Unis]Source :
- Systematic Biology [ 1063-5157 ] ; 2014.
Abstract
We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a
Url:
DOI: 10.1093/sysbio/syu031
PubMed: 24789072
PubMed Central: 4141202
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0</title><author><name sortKey="Bazinet, Adam L" sort="Bazinet, Adam L" uniqKey="Bazinet A" first="Adam L." last="Bazinet">Adam L. Bazinet</name><affiliation wicri:level="4"><nlm:aff wicri:cut=", and" id="AFF1">Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360</wicri:regionArea><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Zwickl, Derrick J" sort="Zwickl, Derrick J" uniqKey="Zwickl D" first="Derrick J." last="Zwickl">Derrick J. Zwickl</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088</wicri:regionArea><wicri:noRegion>85721-0088</wicri:noRegion></affiliation></author><author><name sortKey="Cummings, Michael P" sort="Cummings, Michael P" uniqKey="Cummings M" first="Michael P." last="Cummings">Michael P. Cummings</name><affiliation wicri:level="4"><nlm:aff wicri:cut=", and" id="AFF1">Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360</wicri:regionArea><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24789072</idno><idno type="pmc">4141202</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141202</idno><idno type="RBID">PMC:4141202</idno><idno type="doi">10.1093/sysbio/syu031</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000665</idno><idno type="wicri:Area/Pmc/Curation">000665</idno><idno type="wicri:Area/Pmc/Checkpoint">000245</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0</title><author><name sortKey="Bazinet, Adam L" sort="Bazinet, Adam L" uniqKey="Bazinet A" first="Adam L." last="Bazinet">Adam L. Bazinet</name><affiliation wicri:level="4"><nlm:aff wicri:cut=", and" id="AFF1">Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360</wicri:regionArea><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Zwickl, Derrick J" sort="Zwickl, Derrick J" uniqKey="Zwickl D" first="Derrick J." last="Zwickl">Derrick J. Zwickl</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088</wicri:regionArea><wicri:noRegion>85721-0088</wicri:noRegion></affiliation></author><author><name sortKey="Cummings, Michael P" sort="Cummings, Michael P" uniqKey="Cummings M" first="Michael P." last="Cummings">Michael P. Cummings</name><affiliation wicri:level="4"><nlm:aff wicri:cut=", and" id="AFF1">Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360</wicri:regionArea><orgName type="university">Université du Maryland</orgName><placeName><settlement type="city">College Park (Maryland)</settlement><region type="state">Maryland</region></placeName></affiliation></author></analytic><series><title level="j">Systematic Biology</title><idno type="ISSN">1063-5157</idno><idno type="eISSN">1076-836X</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a <sc>garli</sc> 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The <sc>garli</sc> web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the <sc>garli</sc> web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [<sc>garli</sc>, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.]</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Anderson, D P" uniqKey="Anderson D">D.P. Anderson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bazinet, A L" uniqKey="Bazinet A">A.L. Bazinet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bazinet, A L" uniqKey="Bazinet A">A.L. Bazinet</name></author><author><name sortKey="Cummings, M P" uniqKey="Cummings M">M P. Cummings</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bazinet, A L" uniqKey="Bazinet A">A.L. Bazinet</name></author><author><name sortKey="Cummings, M P" uniqKey="Cummings M">M.P. Cummings</name></author><author><name sortKey="Mitter, K T" uniqKey="Mitter K">K.T. Mitter</name></author><author><name sortKey="Mitter, C W" uniqKey="Mitter C">C.W. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Syst Biol</journal-id><journal-id journal-id-type="iso-abbrev">Syst. Biol</journal-id><journal-id journal-id-type="publisher-id">sysbio</journal-id><journal-id journal-id-type="hwp">sysbio</journal-id><journal-title-group><journal-title>Systematic Biology</journal-title></journal-title-group><issn pub-type="ppub">1063-5157</issn><issn pub-type="epub">1076-836X</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24789072</article-id><article-id pub-id-type="pmc">4141202</article-id><article-id pub-id-type="doi">10.1093/sysbio/syu031</article-id><article-id pub-id-type="publisher-id">syu031</article-id><article-categories><subj-group subj-group-type="heading"><subject>Software for Systematics and Evolution</subject></subj-group></article-categories><title-group><article-title>A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Bazinet</surname><given-names>Adam L.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Zwickl</surname><given-names>Derrick J.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Cummings</surname><given-names>Michael P.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><aff id="AFF1"><sup>1</sup>Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742-3360, USA, and<sup>2</sup>Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA</aff></contrib-group><author-notes><corresp id="COR1">*Correspondence to be sent to: Center for Bioinformatics and Computational Biology, University of Maryland, Biomolecular Sciences Building, College Park, MD, 20742-3360, USA; E-mail: <email>adam.bazinet@umiacs.umd.edu</email>.</corresp><fn id="FN100"><p>Associate Editor: David Posada</p></fn></author-notes><pub-date pub-type="ppub"><month>9</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>30</day><month>4</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>30</day><month>4</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>63</volume><issue>5</issue><fpage>812</fpage><lpage>818</lpage><history><date date-type="received"><day>2</day><month>2</month><year>2014</year></date><date date-type="rev-request"><day>21</day><month>3</month><year>2014</year></date><date date-type="accepted"><day>22</day><month>4</month><year>2014</year></date></history><permissions><copyright-statement>© The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.</copyright-statement><copyright-year>2014</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<uri xlink:type="simple" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">http://creativecommons.org/licenses/by-nc/3.0/</uri>), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.</license-p></license></permissions><abstract><p>We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a <sc>garli</sc> 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The <sc>garli</sc> web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the <sc>garli</sc> web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [<sc>garli</sc>, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.]</p></abstract><counts><page-count count="7"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region><settlement><li>College Park (Maryland)</li></settlement><orgName><li>Université du Maryland</li></orgName></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="Bazinet, Adam L" sort="Bazinet, Adam L" uniqKey="Bazinet A" first="Adam L." last="Bazinet">Adam L. Bazinet</name></region><name sortKey="Cummings, Michael P" sort="Cummings, Michael P" uniqKey="Cummings M" first="Michael P." last="Cummings">Michael P. Cummings</name><name sortKey="Zwickl, Derrick J" sort="Zwickl, Derrick J" uniqKey="Zwickl D" first="Derrick J." last="Zwickl">Derrick J. Zwickl</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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