View source: R/f_phyclust_edist.r
phyclust.edist | R Documentation |
This computes pair wised evolution distance of sequences.
phyclust.edist(X, edist.model = .edist.model[1])
X |
nid/sid matrix with |
edist.model |
evolution distance model. |
X
should be a numerical matrix containing sequence data that
can be transfered by code2nid
or code2sid
.
This function returns a object with class dist
.
incorporate dist.dna
of ape.
Wei-Chen Chen wccsnow@gmail.com
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
.edist.model
.
## 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)
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