common_ancestor()
create_dichotomic_sister()insert_intermediate()interchange_references()join_branch()ladderize()make_name()populate_yule()
rehang()remove()root_at()set_outgroup()sort()swap_props()Insert, between node and its parent, an intermediate node.
Interchange the references of the given nodes.
+Rehang node on its child at position child_pos and return it.
+Rehang root on its child at position child_pos and return it.
Remove the given node from its tree.
Set the given node as the root of the tree.
+The original root node will be used as the new root node, so any +reference to it in the code will still be valid.
+node – Node to set as root. Its reference will be lost.
bprops – List of branch properties (other than “dist” and “support”).
Reroot the tree at the given outgroup node.
+Change tree so the given node is set as outgroup.
The original root node will be used as the new root node, so any reference to it in the code will still be valid.
node – Node where to set root (future first child of the root).
node – Node to set as outgroup (future first child of the root).
bprops – List of branch properties (other than “dist” and “support”).
Reroot the tree at the given outgroup node.
+Change tree so the given node is set as outgroup.
+The original root node will be used as the new root node, so any +reference to it in the code will still be valid.
+node – Node to set as outgroup (future first child of the root).
bprops – List of branch properties (other than “dist” and “support”).
Unroot current node.
-This function is expected to be used on the absolute tree root -node, but it can be also be applied to any other internal -node. It will convert a split into a multifurcation.
-mode – The value can be “legacy” or “keep”. If value is -“keep”, it keeps the distance between the leaves by adding -the distance associated to the deleted edge to the -remaining edge. Otherwise that distance is just dropped.
-Unroot the tree, that is, make the root not have 2 children.
+The convention in phylogenetic trees is that if the root has 2 +children, it is a “rooted” tree (the root is a real ancestor). +Otherwise (typically a root with 3 children), the root is just +an arbitrary place to hang the tree.