My question is in regards to the hmmsearch/hmmalign commands of the HMMER program. As an output, both of these commands produce a sequence alignment with respect to the HMM that was used to query the sequence database. My question is, from the aligned domain sequences that can then be extracted, would it at all be necessary to use a conventional multiple-sequence algorithm to realign the domain sequences (extracted)?
My thinking is that by using the most accurate algorithms (e.g. MAFFT L-INS-i), a more reliable alignment would be produced -- in an analogous sense to still using an MSA algorithm to align the output of a BLAST search, even though the output is itself an alignment? Not sure whether this would be necessary or not.