seqinr (version 1.0-2)

dist.alignment: Pairwise Distances from Aligned Protein or DNA/RNA Sequences

Description

These functions compute a matrix of pairwise distances from aligned sequences using similarity (Fitch matrix) or identity matrix.

Usage

dist.alignment(x, matrix = "similarity")

Arguments

x

object of class alignment

matrix

the matrix distance to be used: "similarity" or "identity"

Value

• The distance matrix, object of class dist, computed by using the specified distance measure.

References

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.

See Also

read.alignment

Examples

s = read.alignment(File=system.file("sequences/test.mase", package = "seqinr"), format="mase")
 dist.alignment( s, matrix = "identity" )