calc.null.pboot: Calculate the null distribution of the Dss statistic using...

Description Usage Arguments Value Author(s) References See Also

Description

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.

Usage

1
calc.null.pboot(data, B, l, m, exhaustive=F, codeml="codeml", evolver="evolverNSsites 6")

Arguments

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

Value

A vector of numeric values, representing the maximum Dss statistic at each bootstrap replicate.

Author(s)

Peter Chi pchi@calpoly.edu

References

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.

See Also

calc.Dss.all, calc.null.pboot.syn


synDss documentation built on May 2, 2019, 5:40 p.m.