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TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.

Iain Milne·Frank Wright·Glenn Rowe·David F Marshall·Dirk Husmeier·Gràinne McGuire
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Abstract

SUMMARY: TOPALi is a new Java graphical analysis application that allows the user to identify recombinant sequences within a DNA multiple alignment (either automatically or via manual investigation). TOPALi allows a choice of three statistical methods to predict the positions of breakpoints due to past recombination. The breakpoint predictions are then used to identify putative recombinant sequences and their relationships to other sequences. In addition to its sophisticated interface, TOPALi can import many sequence formats, estimate and display phylogenetic trees and allow interactive analysis and/or automatic HTML report generation. AVAILABILITY: TOPALi is freely available from http://www.bioss.ac.uk/software.html

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Computer GraphicsGene Expression ProfilingInformation Storage and RetrievalOnline SystemsPattern Recognition, AutomatedPhylogenyProgramming LanguagesRecombination, GeneticSequence AlignmentSequence Analysis, DNASoftwareUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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Iain Milne, Frank Wright, Glenn Rowe, David F Marshall, Dirk Husmeier, Gràinne McGuire. 2004-02-26. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments.. https://doi.org/10.1093/bioinformatics%2Fbth155

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