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Nucleic Acids Research Advance Access originally published online on December 6, 2006
Nucleic Acids Research 2007 35(Database issue):D328-D331; doi:10.1093/nar/gkl905
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Nucleic Acids Research, 2007, Vol. 35, Database issue D328-D331
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

GeneTrees: a phylogenomics resource for prokaryotes

Yuying Tian and Allan W. Dickerman*

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA 24061, USA

*To whom correspondence should be addressed. Tel: +1 540 231 1397; Fax: +1 540 231 2606; Email: dickerman{at}vt.edu

Received August 15, 2006. Revised October 11, 2006. Accepted October 12, 2006.

The 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.


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J. Huerta-Cepas, A. Bueno, J. Dopazo, and T. Gabaldon
PhylomeDB: a database for genome-wide collections of gene phylogenies
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D491 - D496.
[Abstract] [Full Text] [PDF]


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