pairwiseDist - Calculate pairwise distances between sequences

## Description¶

`pairwiseDist` calculates all pairwise distance between a set of sequences.

## Usage¶

``````pairwiseDist(seq, dist_mat = getDNAMatrix())
``````

## Arguments¶

seq
character vector containing a DNA sequences.
dist_mat
Character distance matrix. Defaults to a Hamming distance matrix returned by getDNAMatrix. If gap characters, `c("-", ".")`, are assigned a value of -1 in `dist_mat` then contiguous gaps of any run length, which are not present in both sequences, will be counted as a distance of 1. Meaning, indels of any length will increase the sequence distance by 1. Gap values other than -1 will return a distance that does not consider indels as a special case.

## Value¶

A matrix of numerical distance between each entry in `seq`. If `seq` is a named vector, row and columns names will be added accordingly.

## Examples¶

``````# Gaps will be treated as Ns with a gap=0 distance matrix
pairwiseDist(c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C"),
dist_mat=getDNAMatrix(gap=0))

``````
``````  A B C D
A 0 1 1 0
B 1 0 0 1
C 1 0 0 1
D 0 1 1 0

``````
``````
# Gaps will be treated as universally non-matching characters with gap=1
pairwiseDist(c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C"),
dist_mat=getDNAMatrix(gap=1))

``````
``````  A B C D
A 0 1 1 2
B 1 0 0 3
C 1 0 0 3
D 2 3 3 0

``````
``````
# Gaps of any length will be treated as single mismatches with a gap=-1 distance matrix
pairwiseDist(c(A="ATGGC", B="ATGGG", C="ATGGG", D="AT--C"),
dist_mat=getDNAMatrix(gap=-1))
``````
``````  A B C D
A 0 1 1 1
B 1 0 0 2
C 1 0 0 2
D 1 2 2 0

``````