treetime/treeanc.py
def sequence_LH(self, pos=None, full_sequence=False):
        """return the likelihood of the observed sequences given the tree

        Parameters
        ----------
        pos : int, optional
            position in the sequence, if none, the sum over all positions will be returned
        full_sequence : bool, optional
            does the position refer to the full or compressed sequence, by default compressed sequence is assumed.

        Returns
        -------
        float
            likelihood
        """
        if not hasattr(self.tree, "total_sequence_LH"):
            self.logger("TreeAnc.sequence_LH: you need to run marginal ancestral inference first!", 1)
            self.infer_ancestral_sequences(marginal=True)
        if pos is not None:
            if full_sequence:
                compressed_pos = self.full_to_reduced_sequence_map[pos]
            else:
                compressed_pos = pos
            return self.tree.sequence_LH[compressed_pos]
        else:
            return self.tree.total_sequence_LH
def sequence_LH(self, pos=None, full_sequence=False):
        if not hasattr(self.tree, "total_sequence_LH"):
            self.logger("TreeAnc.sequence_LH: you need to run marginal ancestral inference first!", 1)
            self.infer_ancestral_sequences(marginal=True)
        if pos is not None:
            if full_sequence:
                compressed_pos = self.full_to_reduced_sequence_map[pos]
            else:
                compressed_pos = pos
            return self.tree.sequence_LH[compressed_pos]
        else:
            return self.tree.total_sequence_LH
def sequence_LH ( self , pos = None , full_sequence = False ) : if not hasattr ( self . tree , "total_sequence_LH" ) : self . logger ( "TreeAnc.sequence_LH: you need to run marginal ancestral inference first!" , 1 ) self . infer_ancestral_sequences ( marginal = True ) if pos is not None : if full_sequence : compressed_pos = self . full_to_reduced_sequence_map [ pos ] else : compressed_pos = pos return self . tree . sequence_LH [ compressed_pos ] else : return self . tree . total_sequence_LH
return the likelihood of the observed sequences given the tree

        Parameters
        ----------
        pos : int, optional
            position in the sequence, if none, the sum over all positions will be returned
        full_sequence : bool, optional
            does the position refer to the full or compressed sequence, by default compressed sequence is assumed.

        Returns
        -------
        float
            likelihood
return the likelihood of the observed sequences given the tree