tskit uses a combinatorial approach to identify unique topologies of rooted, leaf-labelled trees. It provides methods for enumerating all possible tree topologies, as well as converting back and forth between a tree and its position, or rank, in the enumeration of all possible topologies. These methods do not only apply to binary trees; rather, they cover general, rooted trees without unary nodes.


Return the rank of this tree.


Return a Tree given its rank and a number of leaves.


Return a generator over all leaf-labelled trees of n leaves.


Return a generator over all tree shapes of n leaves.


Return a generator over all labellings of the given tree’s shape.

Interpreting Tree Ranks

To understand tree ranks we must look at how leaf-labelled tree topologies are enumerated. For example, we can use tskit.all_trees() to generate all possible topologies of three leaves:

for t in tskit.all_trees(num_leaves=3):
    display(SVG(t.draw(node_labels={0: 0, 1: 1, 2: 2}, order="tree")))
_images/topology_0_0.svg _images/topology_1_0.svg _images/topology_1_1.svg _images/topology_1_2.svg

In this sequence, there exist two distinct tree shapes and each shape can be labelled in at least one unique way. Given that topologies are ordered first by their shape and then by their labelling, a tree topology can be uniquely identified by

  1. The shape of the tree

  2. The labelling of the tree’s shape

We can refer to the first tree in the above enumeration as the first labelling of the first shape of trees with three leaves, or tree \((0, 0)\). The second tree can be identified as the first labelling of the second shape, or \((1, 0)\), and so on. This pair of indexes for the shape and labelling of a tree is referred to as the rank of the tree, and can be computed using the Tree.rank() method.

ranks = [t.rank() for t in tskit.all_trees(num_leaves=3)]
print("Ranks of 3-leaf trees:", ranks)
Ranks of 3-leaf trees: [(0, 0), (1, 0), (1, 1), (1, 2)]


Ranks in combinatorics are typically natural numbers. However, we refer to this tuple of shape and label rank as a rank because it serves the same purpose of indexing trees in an enumeration.

For details on how shapes and labellings are ordered, see Enumerating Topologies.

We can also reconstruct a leaf-labelled tree given its rank. This process is known as unranking, and can be performed using the Tree.unrank() method.

for rank in [(0, 0), (1, 0), (1, 1), (1, 2)]:
    t = Tree.unrank(3, rank)
    display(SVG(t.draw(node_labels={0: 0, 1: 1, 2: 2}, order="tree")))
_images/topology_0_0.svg _images/topology_1_0.svg _images/topology_1_1.svg _images/topology_1_2.svg


One application of tree ranks is to count the different leaf-labelled topologies in a tree sequence. Since the ranks are just tuples, we can use a Python Counter to track them. Here, we count and unrank the most frequently seen topology in a tree sequence. For brevity, this example assumes samples are synonymous with leaves.

rank_counts = collections.Counter(t.rank() for t in ts.trees())
most_freq_rank, count = rank_counts.most_common(1)[0]
Tree.unrank(ts.num_samples(), most_freq_rank)

Enumerating Topologies

This section expands briefly on the approach used to enumerate tree topologies that serves as the basis for Tree.rank() and Tree.unrank(). To enumerate all rooted, leaf-labelled tree topologies, we first formulate a system of ordering and enumerating tree shapes. Then we define an enumeration of labellings given an arbitrary tree shape.

Enumerating Tree Shapes

Starting with \(n = 1\), we see that the only shape for a tree with a single leaf is a single root leaf. A tree with \(n > 1\) leaves can be obtained by joining at least two trees whose number of leaves sum to \(n\). This maps very closely to the concept of integer partitions. Each tree shape of \(n\) leaves can be represented by taking a nondecreasing integer partition of \(n\) (elements of the partition are sorted in nondecreasing order) and recursively partitioning its elements. The order in which we select partitions of \(n\) is determined by the efficient rule_asc algorithm for generating them.

All tree shapes with four leaves, and the partitions that generate them, are:

All four-leaf tree shapes and their generating partitions

Note that the middle column reflects all tree shapes of three leaves in the right subtree!

* This excludes the partition [\(n\)], since this would create a unary node and trees with unary nodes are inumerable (and potentially infinite).


Using nondecreasing integer partitions enforces a canonical orientation on the tree shapes, where children under a node are ordered by the number of leaves below them. This is important because it prevents us from repeating trees that are topologically the same but whose children are ordered differently.

Labelling Tree Shapes

Tree shapes are useful in and of themselves, but we can use the enumeration formulated above to go further and assign labels to the leaves of each shape.

Say we are given a tree \(T\) with \(n\) leaves, whose left-most subtree, \(T_l\), has k leaves. For each of the \(n \choose k\) ways to select labels to assign to \(T_l\), we produce a unique labelling of \(T\). This process of choosing labels is repeated for the other children of \(T\) and then recursively for the subtrees.

Looking back to the example from Interpreting Tree Ranks, we can see the different unique ways to label a particular tree of three leaves.

_images/topology_1_0.svg _images/topology_1_1.svg _images/topology_1_2.svg

The order of the tree labellings is a direct result of the way in which combinations of labels are chosen. The implementation in tskit uses a standard lexicographic ordering to choose labels. See how the trees are sorted by the order in which the left leaf’s label was chosen.


There is a caveat here regarding symmetry, similar to that of repeating tree shapes. Symmetrical trees run the risk of creating redundant labellings if all combinations of labels were exhausted. To prevent redundant labellings we impose a canonical labelling. In the case of two symmetrical subtrees, the left subtree must receive the minimum label from the label set. Notice how this is the case in the right subtrees above.

These two enumerations create a complete ordering of topologies where trees are ordered first by size (number of leaves), then by shape, then by their minimum label. It is this canonical order that enables efficient ranking and unranking of topologies.