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Table 2 Description of the output files created. Examples for the organisms analyzed here can be found at

From: Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays

File Name Content Description
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.