Enumerating Unrooted Binary Trees solved by 120

April 17, 2013, 6 p.m. by Rosalind Team

Topics: Combinatorics, Phylogeny

Seeing the Forest

In “Counting Unrooted Binary Trees”, we found a way to count the number of unrooted binary trees representing phylogenies on $n$ taxa. Our observation was that two such trees are considered distinct when they do not share the same collection of splits.

Counting all these trees is one task, but actually understanding how to write them out in a list (i.e., enumerating them) is another, which will be the focus of this problem.

Problem

Figure 1. This unrooted binary tree may be represented in Newick format by (((a,b),c),(d,e)); another way of encoding it is ((a,b),(c,(d,e))).

Recall the definition of Newick format from “Distances in Trees” as a way of encoding trees. See Figure 1 for an example of Newick format applied to an unrooted binary tree whose five leaves are labeled (note that the same tree can have multiple Newick representations).

Given: A collection of species names representing $n$ taxa.

Return: A list containing all unrooted binary trees whose leaves are these $n$ taxa. Trees should be given in Newick format, with one tree on each line; the order of the trees is unimportant.

Sample Dataset

dog cat mouse elephant

Sample Output

(((mouse,cat),elephant))dog;
(((elephant,mouse),cat))dog;
(((elephant,cat),mouse))dog;

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