R: Pairwise Distances from Aligned Protein or DNA/RNA Sequences

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, 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.

### Usage

    dist.alignment(x, matrix = c("similarity", "identity"),gap)

### Arguments

`x` | an object of class `alignment`, as returned by `read.alignment` for instance
`matrix` | the matrix distance to be used, partial matching allowed
`gap` | -optional- with nucleotides, if set to 1, gaps will be counted in the identity measure

### Value

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

### Author(s)

D. Charif, J.R. Lobry

### References

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")`

### See Also

`read.alignment`

### Examples

     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" ))

[Package seqinr version 3.4-5 Index]