I searched the uniprot database by hmmsearch using a custom alignment built from selected sequence. Now I am wondering if it will be a good idea to realign the hits using Muscle or just use the hmmsearch results for building phylogenetic tree. Also should I remove the columns with >33% gap in the MSA before building the phylogenetic tree?
1 answer
What you have from your search is a multiple pairwise alignment (sequences aligned to a reference, one-vs-all relationship). Phylogenetic trees basically by definition require multiple sequence alignment (they represent all-vs-all relationship), so yes, you need to re-align the hits using MUSCLE, MAFFT or whatever else is there for calculation of MSA.
It all depends on the question you are asking (and whether your sequence was a fragment, single-domain protein, multi-domain protein, etc.). In the most simple case, if you just used hmmsearch to find remote homologs of your query protein, take out full sequences of the hits and realign them with Muscle/MAFFT. And _again_: what you got from hmmsearch is _not_ MSA.
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