View source: R/dist.alignment.R
dist.alignment | R Documentation |
These functions compute a matrix of pairwise distances from aligned sequences using similarity (Fitch matrix, for protein sequences only) or identity matrix (for protein and DNA sequences). The resulting matrix contains the squared root of the pairwise distances. For example, if identity between 2 sequences is 80 the squared root of (1.0 - 0.8) i.e. 0.4472136. Note: seqinr::dist.alignment is the square root version of ape::dist.gene (and not ape::dist.dna).
dist.alignment(x, matrix = c("identity", "similarity"),gap)
x |
an object of class |
matrix |
the matrix distance to be used, partial matching allowed |
gap |
-optional- logical, with identity matrix, if set to |
The distance matrix, object of class dist
, computed by using the
specified distance measure.
D. Charif, J.R. Lobry
The reference for the similarity matrix is :
Fitch, W.M. (1966) An improved method of testing for evolutionary homology.
J. Mol. Biol., 16:9-16.
citation("seqinr")
read.alignment
myseqs <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase") dist.alignment(myseqs, matrix = "identity" ) as.matrix(dist.alignment(myseqs, matrix = "identity" ))
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