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Strimmer, K.; Forslund, K.; Holland, B.; Moulton, V.: A novel exploratory method for visual recombination detection. In: Genome Biology 2003, 4:R33
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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.