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Bioinformatics. 2004 Jul 22;20(11):1806-7. Epub 2004 Feb 26.

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

Author information

1
Biomathematics & Statistics Scotland, SCRI, Dundee, DD2 5DA, UK. topali@bioss.ac.uk

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

PMID:
14988107
DOI:
10.1093/bioinformatics/bth155
[Indexed for MEDLINE]

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