treetime/treeanc.py
def prune_short_branches(self):
        """
        If the branch length is less than the minimal value, remove the branch
        from the tree. **Requires** ancestral sequence reconstruction
        """
        self.logger("TreeAnc.prune_short_branches: pruning short branches (max prob at zero)...", 1)
        for node in self.tree.find_clades():
            if node.up is None or node.is_terminal():
                continue

            # probability of the two seqs separated by zero time is not zero
            if self.gtr.prob_t(node.up.cseq, node.cseq, 0.0,
                               pattern_multiplicity=self.multiplicity) > 0.1:
                # re-assign the node children directly to its parent
                node.up.clades = [k for k in node.up.clades if k != node] + node.clades
                for clade in node.clades:
                    clade.up = node.up
def prune_short_branches(self):
        """
        If the branch length is less than the minimal value, remove the branch
        from the tree. **Requires** ancestral sequence reconstruction
        """
        self.logger("TreeAnc.prune_short_branches: pruning short branches (max prob at zero)...", 1)
        for node in self.tree.find_clades():
            if node.up is None or node.is_terminal():
                continue

            # probability of the two seqs separated by zero time is not zero
            if self.gtr.prob_t(node.up.cseq, node.cseq, 0.0,
                               pattern_multiplicity=self.multiplicity) > 0.1:
                # re-assign the node children directly to its parent
                node.up.clades = [k for k in node.up.clades if k != node] + node.clades
                for clade in node.clades:
                    clade.up = node.up
If the branch length is less than the minimal value, remove the branch
        from the tree. **Requires** ancestral sequence reconstruction