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