1. A computer-implemented method for reconstructing evolutionary data of a set of haplotype data, comprising the steps of: providing a system, wherein the system comprises distinct software components, each of the distinct software components being embodied on a tangible computer-readable recordable storage medium; obtaining two or more sets of haplotype data, wherein each set of haplotype data comprises a graph, and wherein obtaining two or more sets of haplotype data is carried out by a software component executing on a hardware processor; determining a chronological order of one or more mutations within the two or more sets of haplotype data by applying a heuristic-free combinatorial algorithm to each set of haplotype data, wherein determining a chronological order of one or more mutations is carried out by a software component executing on a hardware processor; determining a chronological order of one or more recombinations within the two or more sets of haplotype data by applying a heuristic-free combinatorial algorithm to each set of haplotype data, wherein determining a chronological order of one or more recombinations is carried out by a software component executing on a hardware processor; determining a position of each recombination within the two or more sets of haplotype data, wherein determining a position of each recombination is carried out by a software component executing on a hardware processor; and combining the chronological order of the one or more mutations, the chronological order of the one or more recombinations and the position of each recombination to reconstruct evolutionary data of the two or more sets of haplotype data to determine relatedness of the two or more sets of haplotype data via generating a consensus graph via a consensus algorithm to infer topology of the haplotype data, wherein the consensus graph is generated from the two or more graphs of haplotype data, and wherein topology of the haplotype data comprises an ordering the one or more mutations and the one or more recombinations in the haplotype data, wherein combining the chronological order of the one or more mutations, the chronological order of the one or more recombinations and the position of each recombination to reconstruct evolutionary data of the two or more sets of haplotype data is carried out by a software component executing on a hardware processor.