calc.null.pboot: Calculate the null distribution of the Dss statistic using...
In synDss: Recombination detection using synonymous distances

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

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