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PMID: 12734013 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

A novel exploratory method for visual recombination detection.

Genome biology ·Vol. 4 ·No. 5 ·2003-00-00 ·Pages R33

Strimmer K, Forslund K, Holland B, Moulton V

Abstract

A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. The method is based on two novel diagrams - the highway plot and the occupancy plot - that graphically portray phylogenetic inhomogeneity along an alignment, and can be viewed as a synthesis of two widely used but unrelated methods: bootscanning and quartet-mapping. To illustrate the method, simulated data and HIV-1 and influenza A datasets are investigated.

MeSH Terms
Computational Biology/methods Computer Simulation Databases, Genetic HIV-1/genetics Humans Models, Genetic Orthomyxoviridae/genetics Phylogeny Recombination, Genetic/genetics Sequence Alignment/methods
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Strimmer Korbinian
Department of Statistics, University of Munich, Germany. strimmer@stat.uni-muenchen.de
Forslund Kristoffer
Holland Barbara
Moulton Vincent
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2003-4-5-r33
Email
strimmer@stat.uni-muenchen.de
Published
2003-00-00
Epub
2003-00-25
Pages
R33
Language
English
Region
England
NLM ID
100960660
PMCID
PMC156589
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2003-4-5-r33 PMC Full Text View journal details
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