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A novel exploratory method for visual recombination detection |
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| Authors: | |
| Institution: | (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 |
| 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. |
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