Recently I am using the R package called 'msa', and I have several questions very confused after getting the result.
For my understanding, the last line of MSA result (which title is 'con') is the consensus sequence. In this case, by the handbook of MSA, the consensus residue is the frequency over 80% (by default). Then I am confused about the question mark appear in this line. Is it indicating that in this position we have several candidates which are both in a high frequency?
Since the conserved score (compute by function 'msaConservationScore') is a bit differ from the consensus sequence, how can I know which part of the sequence alignment is matched together? I am guessing maybe the regions which consensus sequence have symbols but not a hyphen (-)?