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.
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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.