Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.
Applications Note |
TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments
1 Biomathematics & Statistics Scotland, SCRI, Dundee, DD2 5DA, UK, 2 Applied Computing, University of Dundee, Dundee, DD1, 4HN, UK, 3 Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, UK and 4 Biomathematics & Statistics Scotland, King's Buildings, Edinburgh, EH9 3JZ, UK
Received on September 24, 2003; revised on December 22, 2003; accepted on January 26, 2004
Advance Access Publication February 26, 2004
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
Contact: topali{at}bioss.ac.uk
* To whom correspondence should be addressed.
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