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A novel exploratory method for visual recombination detection.

Korbinian Strimmer·Kristoffer Forslund·Barbara Holland·Vincent Moulton
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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.

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Computational BiologyComputer SimulationDatabases, GeneticHIV-1HumansModels, GeneticOrthomyxoviridaePhylogenyRecombination, GeneticSequence AlignmentComparative StudyJournal ArticleResearch Support, Non-U.S. Gov't

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Korbinian Strimmer, Kristoffer Forslund, Barbara Holland, Vincent Moulton. 2003-04-25. A novel exploratory method for visual recombination detection.. https://doi.org/10.1186/gb-2003-4-5-r33

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