Maximum parsimony is used to build an evolutionary tree by choosing the "simplest" one. I see a lot of examples about how this should be done. For example:
However it's not clear for me WHICH nucleotide should be used as starting point? Let's consider the first tree(from the figure above):
G was chosen as starting point resulting in one mutation, however if we choose
T we would have two mutations and if we choose
A we would have three. So what determines the nucleotide which should be used to start with?
The "starting point", or ancestral state, is chosen so as to obtain the most parsimonious tree.
Parsimony is used both for choosing the topology and for choosing the ancestral states for a given topology:
1) The parsimony score for a given topology is computed for the set of ancestral states minimizing the number of transformations.
2) Then, the topology minimizing this minimized number of transformations is chosen as the most parsimonious tree.