I think this works. main change is the mutations separately for HA1/HA2 and the signal peptide. option --ATG has no effect, everything is supposed to be in the genbank outgroup. tool tips show mutations as list for different genes. Clade frequencies now directly refer to the frequency of the labeled branch in the tree.
I think this works. main change is the mutations separately for HA1/HA2 and the signal peptide. option --ATG has no effect, everything is supposed to be in the genbank outgroup. tool tips show mutations as list for different genes. Clade frequencies now directly refer to the frequency of the labeled branch in the tree.