nwhamming {dada2} | R Documentation

## Hamming distance after Needlman-Wunsch alignment.

### Description

This function performs a Needleman-Wunsch alignment between two sequences, and then counts the number of mismatches and indels in that alignment. End gaps are not included in this count.

### Usage

    nwhamming(s1, s2, ...)

### Arguments

`s1` | (Required). `character(1)`. The first sequence to align. A/C/G/T only.
`s2` | (Required). `character(1)`. The second sequence to align. A/C/G/T only.
`...` | (Optional). Further arguments to pass on to `nwalign`.

### Value

`integer(1)`. The total number of mismatches and gaps, excluding gaps at the beginning and end of the alignment.

### Examples

     sq1 <- "CTAATACATGCAAGTCGAGCGAGTCTGCCTTGAAGATCGGAGTGCTTGCACTCTGTGAAACAAGATA"
     sq2 <- "TTAACACATGCAAGTCGAACGGAAAGGCCAGTGCTTGCACTGGTACTCGAGTGGCGAACGGGTGAGT"
    nwhamming(sq1, sq2)
    nwhamming(sq1, sq2, band=16)

[Package dada2 version 1.8.0 Index]