Description Usage Arguments Value Author(s) References See Also
This function takes the data, and estimates a null distribution of the Dss statistic using the overall least squares tree as the evolutionary history of the sequences under the null hypothesis.
1 | calc.null.pboot(data, B, l, m, exhaustive=F, codeml="codeml", evolver="evolverNSsites 6")
|
data |
The sequence alignment, as a matrix of A,C,T,G characters |
B |
Number of bootstrap replicates to use |
l |
Step size for the sliding windows (should be the same as what was used for calculation of the Dss statistic) |
m |
Half-window size (total window size will be 2m) |
exhaustive |
Performs exhaustive search if TRUE |
codeml |
Call to codeml executable; can be changed if needed |
evolver |
Call to evolver executable; can be changed if needed |
A vector of numeric values, representing the maximum Dss statistic at each bootstrap replicate.
Peter Chi pchi@calpoly.edu
G. McGuire, F. Wright, and M.J. Prentice. A graphical method for detecting recombination in phylogenetic data sets. Molecular Biology and Evolution, 14:1125-1131, 1997.
calc.Dss.all
, calc.null.pboot.syn
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