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


BACKGROUND
TOPALi is freely available from http://www.bioss.ac.uk/software.html
Biomathematics & Statistics Scotland, SCRI, Dundee, DD2 5DA, UK. topali@bioss.ac.uk
Iain
I
Milne
Frank
F
Wright
Glenn
G
Rowe
David F
DF
Marshall
Dirk
D
Husmeier
Gràinne
G
McGuire
D003196:Computer Graphics; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D009862:Online Systems; D010363:Pattern Recognition, Automated; D010802:Phylogeny; D011381:Programming Languages; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface