If I perform an alignment of 100 sequences but then decide to discard 3 (for example) from my dataset (for whatever reason), do I need to realign the remaining 97? For example performing MSA via mafft. Thanks!
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written
by
Ritter •
1 answer
It depends on what is the downstream application for your alignments. If you are doing it purely for visualization purposes, you probably don't have to re-do the alignment. I would still remove the columns that have only gaps (trimAl can do that). If you are aligning to do phylogenetic analyses, I would re-do the alignment.
A general answer is that it is always a good idea to re-align, except when it is very expensive in terms of time. In your case, aligning 97 sequences can be done very quickly unless they are very long.
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