phyclust.edist {phyclust} | R Documentation |
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 |
edist.model |
evolution distance model. |
Details
X
should be a numerical matrix containing sequence data that
can be transfered by code2nid
or code2sid
.
Value
This function returns a object with class dist
.
ToDo(s)
incorporate
dist.dna
of ape.
Author(s)
Wei-Chen Chen wccsnow@gmail.com
References
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
See Also
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)
## End(Not run)
[Package phyclust version 0.1-34 Index]