A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0
Identifieur interne : 000258 ( Main/Exploration ); précédent : 000257; suivant : 000259A 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><idno type="wicri:Area/Ncbi/Merge">000517</idno><idno type="wicri:Area/Ncbi/Curation">000517</idno><idno type="wicri:Area/Ncbi/Checkpoint">000517</idno><idno type="wicri:doubleKey">1063-5157:2014:Bazinet A:a:gateway:for</idno><idno type="wicri:Area/Main/Merge">000258</idno><idno type="wicri:Area/Main/Curation">000258</idno><idno type="wicri:Area/Main/Exploration">000258</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. Mitter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cummings, M" uniqKey="Cummings M">M. Cummings</name></author><author><name sortKey="Huskamp, J" uniqKey="Huskamp J">J. Huskamp</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Foster, I" uniqKey="Foster I">I. Foster</name></author><author><name sortKey="Kesselman, C" uniqKey="Kesselman C">C. Kesselman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hedges, S B" uniqKey="Hedges S">S.B. Hedges</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kawahara, A" uniqKey="Kawahara A">A. Kawahara</name></author><author><name sortKey="Ohshima, I" uniqKey="Ohshima I">I. Ohshima</name></author><author><name sortKey="Kawakita, A" uniqKey="Kawakita A">A. Kawakita</name></author><author><name sortKey="Regier, J" uniqKey="Regier J">J. 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Gabaldón</name></author><author><name sortKey="Dopazo, J" uniqKey="Dopazo J">J. Dopazo</name></author><author><name sortKey="Dopazo, H" uniqKey="Dopazo H">H. Dopazo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sohn, J C" uniqKey="Sohn J">J.-C. Sohn</name></author><author><name sortKey="Regier, J C" uniqKey="Regier J">J.C. Regier</name></author><author><name sortKey="Mitter, C" uniqKey="Mitter C">C. Mitter</name></author><author><name sortKey="Davis, D" uniqKey="Davis D">D. Davis</name></author><author><name sortKey="Landry, J F" uniqKey="Landry J">J.-F. Landry</name></author><author><name sortKey="Zwick, A" uniqKey="Zwick A">A. Zwick</name></author><author><name sortKey="Cummings, M P" uniqKey="Cummings M">M.P. Cummings</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sukumaran, J" uniqKey="Sukumaran J">J. Sukumaran</name></author><author><name sortKey="Holder, M T" uniqKey="Holder M">M.T. Holder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zwickl, D J" uniqKey="Zwickl D">D.J. Zwickl</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><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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