phyclust (version 0.1-24)

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)

• incorporate dist.dna of ape.

Details

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

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

.edist.model.

Examples

# NOT RUN {
library(phyclust, quiet = TRUE)

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)
# }