Title: Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method

Authors: Xiaomeng Wu, Xiu-Feng Wan, Gang Wu, Dong Xu, Guohui Lin

Addresses: Bioinformatics Research Group, Department of Computing Science, University of Alberta Edmonton, Alberta T6G 2E8, Canada. ' Department of Microbiology, Miami University Oxford, Ohio 45056, USA. ' Bioinformatics Research Group, Department of Computing Science, University of Alberta Edmonton, Alberta T6G 2E8, Canada. ' Digital Biology Laboratory, Department of Computer Science, University of Missouri, Columbia, Missouri 65211, USA. ' Bioinformatics Research Group, Department of Computing Science, University of Alberta Edmonton, Alberta T6G 2E8, Canada

Abstract: A new method called Complete Composition Vector (CCV), which is a collection of Composition Vectors (CV), is described to infer evolutionary relationships between species using their complete genomic sequences. Such a method bypasses the complexity of performing multiple sequence alignments and avoids the ambiguity of choosing individual genes for species tree construction. It is expected to effectively retain the rich evolutionary information contained in the whole genomic sequence. The method was applied to infer the evolutionary footprints for several datasets that have been previously studied. The final phylogenies were built by an improved clustered Neighbour-Joining method. The generated phylogenetic trees are highly consistent with taxonomy hierarchy and previous studies, with some biologically interesting disagreements.

Keywords: phylogenetic analysis; whole genome phylogeny; composition vectors; neighbour-joining; clustering; bioinformatics; genome signatures.

DOI: 10.1504/IJBRA.2006.010602

International Journal of Bioinformatics Research and Applications, 2006 Vol.2 No.3, pp.219 - 248

Published online: 07 Aug 2006 *

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