Program Description: |
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.
|