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BMC Bioinformatics

, 8:1

First Online: 02 January 2007Received: 26 July 2006Accepted: 02 January 2007


BackgroundIn general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments for instance ambiguous regions are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment.

ResultsIn this paper, HIV Human Immunodeficiency Virus and SIV Simian Immunodeficiency Virus sequence data are used to evaluate this method. The program produces tree topologies that are identical to those obtained by a combination of standard methods detailed in the HIV Sequence Compendium. Manual alignment editing is not necessary at any stage. Furthermore, only one user-specified parameter is needed for constructing trees.

ConclusionThe extensive tests on HIV-SIV subtyping showed that the virus classifications produced by our method are in good agreement with our best taxonomic knowledge, even in non-coding LTR Long Terminal Repeat regions that are not tractable by regular alignment methods due to frequent duplications-insertions-deletions. Our method, however, is not limited to the HIV-SIV subtyping. It provides an alternative tree construction without a time-consuming aligning procedure.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-8-1 contains supplementary material, which is available to authorized users.

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Autor: Gilles Didier - Laurent Debomy - Maude Pupin - Ming Zhang - Alexander Grossmann - Claudine Devauchelle - Ivan Laprevotte


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