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Bioinformatics Advance Access originally published online on May 27, 2004
Bioinformatics 2005 21(10):2329-2335; doi:10.1093/bioinformatics/bth324
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Whole-genome prokaryotic phylogeny

Stefan R. Henz 1, Daniel H. Huson 1,*, Alexander F. Auch 1, Kay Nieselt-Struwe 1 and Stephan C. Schuster 2

1Center for Bioinformatics Tübingen (ZBIT) Sand 14, Tübingen 72076, Germany
2Max-Planck-Institute for Development Biology Spemannstrasse 35, Tübingen, 72076, Germany

*To whom correspondence should be addressed.

Current understanding of the phylogeny of prokaryotes is based on the comparison of the highly conserved small ssu-rRNA subunit and similar regions. Although such molecules have proved to be very useful phylogenetic markers, mutational saturation is a problem, due to their restricted lengths. Now, a growing number of complete prokaryotic genomes are available. This paper addresses the problem of determining a prokaryotic phylogeny utilizing the comparison of complete genomes. We introduce a new strategy, GBDP, ‘genome blast distance phylogeny’, and show that different variants of this approach robustly produce phylogenies that are biologically sound, when applied to 91 prokaryotic genomes. In this approach, first BLAST is used to compare genomes, then a distance matrix is computed, and finally a tree- or network-reconstruction method such as UPGMA, Neighbor-Joining, BioNJ or Neighbor-Net is applied.

Contact: huson{at}informatik.uni-tuebingen.de


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