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
Milne
Iain
I
Biomathematics & Statistics Scotland, SCRI, Dundee, DD2 5DA, UK. topali@bioss.ac.uk
Wright
Frank
F
Rowe
Glenn
G
Marshall
David F
DF
Husmeier
Dirk
D
McGuire
Gràinne
G
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