dendropy.treemanip – Tree Manipulation

Functions and classes for manipulating or changing tree structural relations.

dendropy.treemanip.collapse_clade(node)

Collapses all internal edges that are descendants of node.

dendropy.treemanip.collapse_conflicting(subtree_root, split, split_bitmask)

Takes a node that is the root of a subtree. Collapses every edge in the subtree that conflicts with split. This can include the edge subtending subtree_root.

dendropy.treemanip.collapse_edge(edge)

Inserts all children of the head_node of edge as children of the tail_node of edge in the same place in the child_node list that head_node had occupied. The edge length and head_node will no longer be part of the tree.

dendropy.treemanip.prune_leaves_without_taxa(tree, delete_outdegree_one=True)

Removes all terminal nodes that have their taxon attribute set to None.

dendropy.treemanip.prune_taxa(tree, taxa, delete_outdegree_one=True)

Removes terminal nodes associated with Taxon objects given by the container taxa (which can be any iterable, including a TaxonSet object) from tree.

dendropy.treemanip.randomly_reorient_tree(tree, rng=None, splits=False)

Randomly picks a new rooting position and rotates the branches around all internal nodes in the tree. If splits is True, the the split_bitmask and split_edges attributes kept valid.

dendropy.treemanip.randomly_rotate(tree, rng=None)

Randomly rotates the branches around all internal nodes in the tree

dendropy.treemanip.retain_taxa(tree, taxa, delete_outdegree_one=True)

Removes terminal nodes that are not associated with any of the Taxon objects given by taxa (which can be any iterable, including a TaxonSet object) from the tree.