Implement AdditivePhylogeny solved by 305

Sept. 8, 2015, 2:38 a.m. by Rosalind Team

The following recursive algorithm, called AdditivePhylogeny, finds the simple tree fitting an n n additive distance matrix D. We assume that you have already implemented a program Limb(D, j) that computes LimbLength(j) for a leaf j based on the distance matrix D. Rather than selecting an arbitrary leaf j from Tree(D) for trimming, AdditivePhylogeny selects leaf n (corresponding to the last row and column of D).

    if n = 2
        return the tree consisting of a single edge of length D1,2
    limbLength Limb(D, n)
    for j ← 1 to n - 1
        Dj,n ← Dj,n - limbLength
        Dn,j ← Dj,n

    (i,n,k) ← three leaves such that Di,k = Di,n + Dn,k
    remove row n and column n from D
    T ← AdditivePhylogeny(D, n - 1)
    v ← the (potentially new) node in T at distance x from i on the path between i and k
add leaf n back to T by creating a limb (v, n) of length limbLength
    return T

Additive Phylogeny Problem

Construct the simple tree fitting an additive matrix.

Given: n and a tab-delimited n x n additive matrix.

Return: A weighted adjacency list for the simple tree fitting this matrix.

Note on formatting: The adjacency list must have consecutive integer node labels starting from 0. The n leaves must be labeled 0, 1, ..., n-1 in order of their appearance in the distance matrix. Labels for internal nodes may be labeled in any order but must start from n and increase consecutively.

Sample Dataset

0   13  21  22
13  0   12  13
21  12  0   13
22  13  13  0

Sample Output


Extra Dataset

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