Weighted genome trees: Refinements and applications

Uri Gophna, W. Ford Doolittle*, Robert L. Charlebois

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)1305-1316
Number of pages12
JournalJournal of Bacteriology
Issue number4
StatePublished - Feb 2005
Externally publishedYes


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