Algorithm 1.

McAN

Input:

, the number of haplotypes,   , the set of mutations in haplotype ,   , the sampling time of haplotype ,   , the number of samples in haplotype .

Output:

, the minimum-cost arborescence, which is a set of edges.

Step 1 (sort all haplotypes by generating a permutation )

Step 2 (find minimum-cost arborescence )       for each from 0 to ,     for each from to ,      if , then       if , then

break,

end if, end if, end for, end for,   return .