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, an...

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Detalles Bibliográficos
Autores principales: Strimmer, Korbinian, Forslund, Kristoffer, Holland, Barbara, Moulton, Vincent
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2003
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC156589/
https://www.ncbi.nlm.nih.gov/pubmed/12734013
http://dx.doi.org/10.1186/gb-2003-4-5-r33
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author Strimmer, Korbinian
Forslund, Kristoffer
Holland, Barbara
Moulton, Vincent
author_facet Strimmer, Korbinian
Forslund, Kristoffer
Holland, Barbara
Moulton, Vincent
author_sort Strimmer, Korbinian
collection PubMed
description 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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spelling pubmed-1565892003-06-05 A novel exploratory method for visual recombination detection Strimmer, Korbinian Forslund, Kristoffer Holland, Barbara Moulton, Vincent Genome Biol Method 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. BioMed Central 2003 2003-04-25 /pmc/articles/PMC156589/ /pubmed/12734013 http://dx.doi.org/10.1186/gb-2003-4-5-r33 Text en Copyright © 2003 Strimmer et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying andredistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL
spellingShingle Method
Strimmer, Korbinian
Forslund, Kristoffer
Holland, Barbara
Moulton, Vincent
A novel exploratory method for visual recombination detection
title A novel exploratory method for visual recombination detection
title_full A novel exploratory method for visual recombination detection
title_fullStr A novel exploratory method for visual recombination detection
title_full_unstemmed A novel exploratory method for visual recombination detection
title_short A novel exploratory method for visual recombination detection
title_sort novel exploratory method for visual recombination detection
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC156589/
https://www.ncbi.nlm.nih.gov/pubmed/12734013
http://dx.doi.org/10.1186/gb-2003-4-5-r33
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