Table 2 Description of the output files created. Examples for the organisms analyzed here can be found at http://est.llnl.gov/forensics

SNPs_all, FLPs_all

list of all the SNPs or PCR-RFLPs found in the input genomes

genome_groups

lists the genome groupings that correspond to each of the character haplotypes

character_haplotypes

lists the co-segregating SNPs or PCR-RFLPs that characterize each haplotype

all_discriminating_sets

for each genome, lists haplotype combinations ("sets") that will discriminate the specified genome to the maximum degree possible

sim_anneal_results_summary

lists combinations of sets of haplotypes to discriminate all the input genomes to the maximum degree possible using the fewest haplotypes. Each row is a unique combination that has the best score found, where the score is the number of haplotypes required.