Regarding NAST algorithm in alignment step with align.seqs command

1

Hi there!!!
I just found the following line while going through about alignment step with align.seqs command:

iii) to re-insert gaps to the candidate and template pairwise alignments using the NAST algorithm so that the candidate sequence alignment is compatible with the original template alignment.

I am a bit confused about why is this step necessary after alignment is performed with the Needleman-Wunsch algorithm. Can anyone please elaborate the reason?

Many Thanks

2

align.seqs does pairwise alignments between your unaligned sequence and the aligned database sequence that is most similar to the unaligned sequence. By adding back in the missing gaps the algorithm makes sure every sequence is aligned to the same alignment structure regardless of the reference sequence it was aligned to. This allows you to compare each of your aligned sequences to each other for things like calculating distances to generate OTUs.

Pat

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