dist.alignment {seqinr} | R Documentation |
These functions compute a matrix of pairwise distances from aligned sequences using similarity (Fitch matrix) or identity matrix.
dist.alignment(x, matrix = "similarity")
x |
object of class alignment |
matrix |
the matrix distance to be used: "similarity" or "identity" |
The distance matrix, object of class dist
, computed by using the specified distance measure.
D. Charif
The reference for the similarity matrix is :
Fitch, W.M. (1966) Mutation values for the interconversion of amino acid pair.
J. Mol. Biol., 16:9-16.
To have an overview of the seqinR's functionnality, please consult this vignette:
Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical
computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.
s = read.alignment(File=system.file("sequences/test.mase", package = "seqinr"), format="mase") dist.alignment( s, matrix = "identity" )