A novel exploratory method for visual recombination detection.
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.
Strimmer
Korbinian
K
Department of Statistics, University of Munich, Germany. strimmer@stat.uni-muenchen.de
Forslund
Kristoffer
K
Holland
Barbara
B
Moulton
Vincent
V
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D009975:Orthomyxoviridae / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods