treetime/treeanc.py
def marginal_branch_profile(self, node):
        '''
        calculate the marginal distribution of sequence states on both ends
        of the branch leading to node,

        Parameters
        ----------
        node : PhyloTree.Clade
           TreeNode, attached to the branch.


        Returns
        -------
        pp, pc : Pair of vectors (profile parent, pp) and (profile child, pc)
           that are of shape (L,n) where L is sequence length and n is alphabet size.
           note that this correspond to the compressed sequences.
        '''
        parent = node.up
        if parent is None:
            raise Exception("Branch profiles can't be calculated for the root!")
        if not hasattr(node, 'marginal_outgroup_LH'):
            raise Exception("marginal ancestral inference needs to be performed first!")

        pc = node.marginal_subtree_LH
        pp = node.marginal_outgroup_LH
        return pp, pc
def marginal_branch_profile(self, node):
        '''
        calculate the marginal distribution of sequence states on both ends
        of the branch leading to node,

        Parameters
        ----------
        node : PhyloTree.Clade
           TreeNode, attached to the branch.


        Returns
        -------
        pp, pc : Pair of vectors (profile parent, pp) and (profile child, pc)
           that are of shape (L,n) where L is sequence length and n is alphabet size.
           note that this correspond to the compressed sequences.
        '''
        parent = node.up
        if parent is None:
            raise Exception("Branch profiles can't be calculated for the root!")
        if not hasattr(node, 'marginal_outgroup_LH'):
            raise Exception("marginal ancestral inference needs to be performed first!")

        pc = node.marginal_subtree_LH
        pp = node.marginal_outgroup_LH
        return pp, pc
calculate the marginal distribution of sequence states on both ends
        of the branch leading to node,

        Parameters
        ----------
        node : PhyloTree.Clade
           TreeNode, attached to the branch.


        Returns
        -------
        pp, pc : Pair of vectors (profile parent, pp) and (profile child, pc)
           that are of shape (L,n) where L is sequence length and n is alphabet size.
           note that this correspond to the compressed sequences.