Title: Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning
Authors: Lemey, Philippe ×
Lott, Martin
Martin, Darren P
Moulton, Vincent #
Issue Date: Apr-2009
Publisher: Biomed central ltd
Series Title: BMC Bioinformatics vol:10 pages:126
Abstract: Background: Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionary studies, identifying the sequences that exhibit such patterns has received comparatively less attention in the recombination detection framework. Here, we extend a quartet-mapping based recombination detection method to enable identification of recombinant sequences without prior specifications of either query and reference sequences. Through simulations we evaluate different recombinant identification statistics and significance tests. We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences.
ISSN: 1471-2105
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Laboratory of Clinical and Epidemiological Virology (Rega Institute)
× corresponding author
# (joint) last author

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