seqDist - Calculate distance between two sequences

## Description¶

`seqDist` calculates the distance between two DNA sequences.

## Usage¶

``````seqDist(seq1, seq2, dist_mat = getDNAMatrix())
``````

## Arguments¶

seq1
character string containing a DNA sequence.
seq2
character string containing a DNA sequence.
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¶

Numerical distance between `seq1` and `seq2`.

## Examples¶

``````# Ungapped examples
seqDist("ATGGC", "ATGGG")

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`````` 1

``````
``````seqDist("ATGGC", "ATG??")

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`````` 2

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``````
# Gaps will be treated as Ns with a gap=0 distance matrix
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=0))

``````
`````` 0

``````
``````
# Gaps will be treated as universally non-matching characters with gap=1
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=1))

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`````` 2

``````
``````
# Gaps of any length will be treated as single mismatches with a gap=-1 distance matrix
seqDist("ATGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))

``````
`````` 1

``````
``````
# Gaps of equivalent run lengths are not counted as gaps
seqDist("ATG-C", "ATG-C", dist_mat=getDNAMatrix(gap=-1))

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`````` 0

``````
``````
# Overlapping runs of gap characters are counted as a single gap
seqDist("ATG-C", "AT--C", dist_mat=getDNAMatrix(gap=-1))

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`````` 1

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``````seqDist("A-GGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))

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`````` 1

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``````seqDist("AT--C", "AT--C", dist_mat=getDNAMatrix(gap=-1))

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`````` 0

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``````
# Discontiguous runs of gap characters each count as separate gaps
seqDist("-TGGC", "AT--C", dist_mat=getDNAMatrix(gap=-1))
``````
`````` 2

``````