compVectorDist: Calculate composition vector distance

In spiderDev: Species Identity and Evolution in R--development

Description

Returns all possible permutations of DNA sequences of a given length.

Usage

compVectorDist(DNAbin, kval = 6, subBackground = FALSE)

Arguments

DNAbin	An object of class 'DNAbin'.
kval	Numeric. Length of the desired K-strings.Default of 6.
subBackground	Logical. Should the background of random mutations be subtracted? Default of FALSE.

Details

subBackground = TRUE results in a larger distance between specimens, but increases the processor time substantially.

Processor time increases exponentially as kval increases. The function takes approximately 16 seconds with the dolomedes dataset and with kval = 6. Errors are given when kval is less than 3.

Value

A matrix giving the composition vector distance between the sequences in the alignment.

Author(s)

Samuel Brown <[e-mail]>

References

Qi J, Wang B, Hao B-I. 2004. Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach. Journal of Molecular Ecology 58:1–11

See Also

permDNA

Examples

data(dolomedes)

compVectorDist(dolomedes)

compVectorDist(dolomedes, kval = 5)

compVectorDist(dolomedes, kval = 5, subBackground = TRUE)

spiderDev documentation built on May 2, 2019, 5:23 p.m.