dist.alignment {seqinr} | R Documentation

## 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.

### Author(s)

D. Charif

### 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.

`citation("seqinr")`

### See Also

`read.alignment`

### Examples

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

[Package seqinr version 1.0-4 Index]