phyclust (version 0.1-9)

phyclust.edist: Evolution distance of sequences

Description

This computes pair wised evolution distance of sequences.

Usage

phyclust.edist(X, edist.model = .edist.model[1])

Arguments

X

nid/sid matrix with $N$ rows/sequences and $L$ columns/sites.

edist.model

evolution distance model.

Value

• This function returns a object with class dist.

ToDo(s)

• incorporatedist.dnaofape.

Details

X should be a numerical matrix containing sequence data that can be transfered by code2nid or code2sid.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

.edist.model.

Examples

X <- rbind(c(0, 2, 1, 3, 0, 2, 2, 0, 3, 2, 2),
           c(0, 0, 1, 3, 2, 2, 1, 0, 3, 1, 2),
           c(0, 2, 1, 1, 0, 2, 1, 3, 0, 0, 1),
           c(2, 2, 1, 1, 0, 0, 2, 3, 0, 2, 1),
           c(2, 2, 1, 1, 0, 0, 2, 3, 1, 2, 0))
(ret <- phyclust.edist(X, edist.model = "D_HAMMING"))
str(ret)
as.matrix(ret)
plot(nj(ret), type = "u", no.margin = TRUE)