Counting Quartets solved by 127

Dec. 4, 2012, 7:10 a.m. by Rosalind Team

Topics: Combinatorics, Phylogeny

Introduction to Quartet-Based Phylogeny

In “Quartets”, we introduced partial splits modeling partial characters on a collection of taxa. Our aim is to use the quartets inferred from partial splits to construct a phylogeny on the taxa. This procedure is called quartet-based phylogeny.

We could construct a phylogeny directly from a collection of partial splits, but it is not immediately clear how many different splits we would need. Hence, our first question is to ask how many quartets are required to be able to infer a tree; in this problem we will ask the reverse question of how many quartets can be inferred from a known tree.

Problem

A quartet $AB \mid CD$ is consistent with a binary tree $T$ if the quartet can be inferred from one of the splits of $T$ (see “Quartets” for a description of inferring quartets from splits).

Let $q(T)$ denote the total number of quartets that are consistent with $T$.

Given: A positive integer $n$ ($4 \leq n \leq 5000$), followed by an unrooted binary tree $T$ in Newick format on $n$ taxa.

Return: The value of $q(T)$ modulo 1,000,000.

Sample Dataset

6
(lobster,(cat,dog),(caterpillar,(elephant,mouse)));

Sample Output

15

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