Creates network alignments using network constructed from subpopulations after PAC
MAN(sampleIDs, num_PACSupop, smallSubpopCutoff, k_clades)sampleID vector
number of subpopulations learned in PAC step for each sample
Population size cutoff for subpopulations in clade calculation. The small subpopulations will be considered in the refinement step.
number of clades to output before refinement
clades_network_only the clades constructed without small subpopulations (by cutoff) using mutual information network alignments