treetime/treeanc.py
def recover_var_ambigs(self):
        """
        Recalculates mutations using the original compressed sequence for terminal nodes
        which will recover ambiguous bases at variable sites. (See 'get_mutations')

        Once this has been run, infer_gtr and other functions which depend on self.gtr.alphabet
        will not work, as ambiguous bases are not part of that alphabet (only A, C, G, T, -).
        This is why it's left for the user to choose when to run
        """
        for node in self.tree.get_terminals():
            node.mutations = self.get_mutations(node, keep_var_ambigs=True)
def recover_var_ambigs(self):
        """
        Recalculates mutations using the original compressed sequence for terminal nodes
        which will recover ambiguous bases at variable sites. (See 'get_mutations')

        Once this has been run, infer_gtr and other functions which depend on self.gtr.alphabet
        will not work, as ambiguous bases are not part of that alphabet (only A, C, G, T, -).
        This is why it's left for the user to choose when to run
        """
        for node in self.tree.get_terminals():
            node.mutations = self.get_mutations(node, keep_var_ambigs=True)
Recalculates mutations using the original compressed sequence for terminal nodes
        which will recover ambiguous bases at variable sites. (See 'get_mutations')

        Once this has been run, infer_gtr and other functions which depend on self.gtr.alphabet
        will not work, as ambiguous bases are not part of that alphabet (only A, C, G, T, -).
        This is why it's left for the user to choose when to run