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Genome Biol. 2003;4(5):R33. Epub 2003 Apr 25.

A novel exploratory method for visual recombination detection.

Author information

  • 1Department of Statistics, University of Munich, Germany. strimmer@stat.uni-muenchen.de

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.

PMID:
12734013
[PubMed - indexed for MEDLINE]
PMCID:
PMC156589
Free PMC Article

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