Hi, I am now trying to work on the ancestral sequence reconstruction of a protein of interest. I am trying to understand the working principle and have looked into related topics such as parsimony and maximum likelihood etc. to understand how do people deduce the ancestral node (i.e. the likely ancestral aa residue). Consider we have an aligned residue in a sequence like:
. . . A . . . . . . A . . . . . . A . . . . . . A . . . . . . A . . . . . . G . . .
I guess the best model (maximum likelihood) to describe the alignment with the assumption that evolution event is rare (parsimony) would be the ancestral node is "A".
Then I have a dumb question, what is the difference between just compare the % of the aa resiue and pick the aa residue with highest % and the actual procedure of deducing ancestral node with the intense computation with maximum likelihood method?
Thanks a lot!