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Journal of Bacteriology, February 2005, p. 1305-1316, Vol. 187, No. 4
0021-9193/05/$08.00+0     doi:10.1128/JB.187.4.1305-1316.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Weighted Genome Trees: Refinements and Applications{dagger}

Uri Gophna,1 W. Ford Doolittle,1 and Robert L. Charlebois2

Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia,1 NeuroGadgets Inc., Ottawa, Ontario, Canada2

Received 13 April 2004/ Accepted 4 November 2004

There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

* Corresponding author. Mailing address: Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College St., Halifax, Nova Scotia, B3H 1X5, Canada. Phone: (902) 494-2968. Fax: (902) 494-1355. E-mail: ford{at}dal.ca.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, February 2005, p. 1305-1316, Vol. 187, No. 4
0021-9193/05/$08.00+0     doi:10.1128/JB.187.4.1305-1316.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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