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A novel exploratory method for visual recombination detection

Korbinian Strimmer1*, Kristoffer Forslund2, Barbara Holland3 and Vincent Moulton2

Author Affiliations

1 Department of Statistics, University of Munich, Ludwigstrasse 33, D-80539 Munich, Germany

2 The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, 7551 24 Uppsala, Sweden

3 Allan Wilson Centre for Molecular Ecology and Evolution, Private Bag 11222, Palmerston North, New Zealand

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Genome Biology 2003, 4:R33  doi:10.1186/gb-2003-4-5-r33

Published: 25 April 2003


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.