I am confused how the consensus sequence is generated. How can the parameters to calculate consensus sequence (if possible) be configured in programs like Jalview? Because, the default setting in Jalview (I used this program) does not seem to be useful to interpret consensus sequence. I would be interested for example, to ignore the positions that are under-represented in the alignment (having less than 10% coverage). In fact, I want to try the program that works best in working with consensus sequence.
I want to view the consensus sequence in such a format that consensus residue for position with lets say 70% conservation will show the amino acid and rest of the positions will be shown as X. Thus, the consensus sequence will be like. AGXXXXXXXEXXXT, where A,G and T are highly conserved residues in particular MSA position.