I have a questions concerning multiple sequence alignments (msa) building algorithms. Which algorithm is "best", to construct a multiple sequence alignment from a bundle of sequences distantly related?
To specify the question a bit more precisely, if I have a bundle of protein sequences, that are annotated to have the same function, but which don't have a similar (midnight or twighlight zone) amino acid sequence, which algorithm works best to align them? (to find sequences that ought to have the same annotation)
I tried gotoh combined with a center star approach, but this do not seem to be a very good approach. I'm now wondering for an algorithm that in provide "better" multiple sequence alignment than "my" first approach:
- calculating pairwise alighments for each sequence pair with gotoh
- find the sequence, for which the sum of pairwise alignments score to all other sequences is best.
- construct a msa by combining the pairwise alignments of this center sequence.