A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database

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We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution ... continued below

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Dehal, Paramvir S. & Boore, Jeffrey L. August 25, 2005.

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We present here the PhIGs database, a phylogenomic resource for sequenced genomes. Although many methods exist for clustering gene families, very few attempt to create truly orthologous clusters sharing descent from a single ancestral gene across a range of evolutionary depths. Although these non-phylogenetic gene family clusters have been used broadly for gene annotation, errors are known to be introduced by the artifactual association of slowly evolving paralogs and lack of annotation for those more rapidly evolving. A full phylogenetic framework is necessary for accurate inference of function and for many studies that address pattern and mechanism of the evolution of the genome. The automated generation of evolutionary gene clusters, creation of gene trees, determination of orthology and paralogy relationships, and the correlation of this information with gene annotations, expression information, and genomic context is an important resource to the scientific community.

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  • Journal Name: BMC Bioinformatics, Biomed Central; Journal Volume: 7; Related Information: Journal Publication Date: 04/11/2006

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  • Report No.: LBNL--59016
  • Grant Number: DE-AC02-05CH11231
  • Grant Number: NSF:MCB-0242131 ANDEF-0328516
  • Office of Scientific & Technical Information Report Number: 882266
  • Archival Resource Key: ark:/67531/metadc892801

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  • August 25, 2005

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  • Sept. 23, 2016, 2:42 p.m.

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  • Nov. 30, 2017, 7:12 p.m.

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Dehal, Paramvir S. & Boore, Jeffrey L. A phylogenomic gene cluster resource: The phylogeneticallyinferred groups (PhlGs) database, article, August 25, 2005; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc892801/: accessed December 17, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.