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doi:10.1534/genetics.106.068874
A more recent version of this article appeared on June 1, 2007.
REGULAR RESEARCH PAPERS |
An exact nonparametric method for inferring mosaic structure in sequence triplets
Maciej F Boni 1*, David Posada 2 and Marcus W. Feldman 1
1 Stanford University
2 University of Vigo
* To whom correspondence should be addressed. E-mail: maciek{at}charles.stanford.edu.
Submitted on November 27, 2006
Revised on January 21, 2007
Accepted on 18 March 2007
Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test which is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences which may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic 
m,n,b. We present a method for rapidly calculating the distribution of m,n,b and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets.
Key Words: Neisseria, hypergeometric random walk, influenza, mosaic structure, recombination detection
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