ABCC : Application's document Page

Topal

2.03b

Phylogenetic Analysis, Bioinformatics

Gráinne McGuire(1) and Frank Wright(2) 
(1) Department of Applied Statistics, University of
Reading 
(2) Biomathematics and Statistics Scotland

email contact: frank@bioss.sari.ac.uk 

TOPAL checks for evidence of past recombination events, by looking
for changes in the inferred phylogenetic tree topology between
adjacent regions of a multiple sequence alignment. It detects
recombinations by sliding a window along a sequence alignment, and
measuring the discrepancy between the trees suggested by the first
and second halves of the window, using distance matrix methods.

Topal method is described in: 
- McGuire, G., F. Wright, and M. J. Prentice. 1997. A graphical
method for detecting recombination in phylogenetic data sets.
Molecular Biology and Evolution 14: 1125-1131. 

The TOPAL 2.0 program, and recent changes to the method, are
described in: 
- McGuire, G. and F. Wright. 2000. TOPAL 2.0 : improved detection of
mosaic sequences within multiple alignments. Bioinformatics 16:
130-134. 

SGI 

/usr/local/fbscapp/Topal2.03b 

Account on SGI systems at ABCC is required.

When using C-shell:
 set path = ($path /usr/local/fbscapp/Topal2.03b)
followed by a name of one of Topal's programs or scripts 

Available locally in HTML format at
/usr/local/fbscapp/Topal2.03b/manual.html.

Also, available on-line at:
http://www.bioss.sari.ac.uk/~frank/Genetics/manual.html 

Bob Stephens
bobs@ncifcrf.gov
301-8465787 

miaskiew

2002-05-24

miaskiew

2002-05-24