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GeneTrees: a phylogenomics resource for prokaryotes

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dc.contributor.authorTian, Yuyingen
dc.contributor.authorDickerman, Allan W.en
dc.date.accessioned2019-04-19T18:32:02Zen
dc.date.available2019-04-19T18:32:02Zen
dc.date.issued2007-01en
dc.description.abstractThe GeneTrees phylogenomics system pursues comparative genomic analyses from the perspective of gene phylogenies for individual genes. The GeneTrees project has the goal of providing detailed evolutionary models for all protein-coding gene components of the fully sequenced genomes. Currently, a database of alignments and trees for all protein sequences for 325 fully sequenced and annotated prokaryote genomes is available. The prokaryote database contains 890 000 protein sequences organized into over 100 000 alignments, each described by a phylogenetic tree. An original homology group discovery tool assembles sets of related proteins from all versus all pairwise alignments. Multiple alignments for each homology group are stored and subjected to phylogenetic tree inference. A graphical web interface provides visual exploration of the GeneTrees database. Homology groups can be queried by sequence identifiers or annotation terms. Genomes can be browsed visually on a gene map of each chromosome or plasmid. Phylogenetic trees with support values are displayed in conjunction with the associated sequence alignment. A variety of classes of information can be selected to label the tree tips to aid in visual evaluation of annotation and gene function. This web interface is available at http://genetrees.vbi.vt.edu.en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1093/nar/gkl905en
dc.identifier.eissn1362-4962en
dc.identifier.issn0305-1048en
dc.identifier.pmid17151073en
dc.identifier.urihttp://hdl.handle.net/10919/89063en
dc.identifier.volume35en
dc.language.isoen_USen
dc.rightsCreative Commons Attribution-NonCommercial 2.0 Genericen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/en
dc.subjectcomparative genomicsen
dc.subjectphylogenetic treesen
dc.subjectdatabaseen
dc.subjectinformationen
dc.subjectorthologyen
dc.subjectinferenceen
dc.subjectalignmenten
dc.subjectmodelsen
dc.subjecttoolen
dc.titleGeneTrees: a phylogenomics resource for prokaryotesen
dc.title.serialNucleic Acids Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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