Table 1 Description of the user-specified parameters for SNP and PCR-RFLP analyses

min_len_upstream

minimum length of conserved sequence upstream (5') of a SNP

min_len_downstream

minimum length of conserved sequence downstream (3') of a SNP

max_amplicon_length

maximum amplicon length allowed for PCR-RFLP analysis

jump

the series of sequences input to primer3 for amplicon generation for PCR-RFLP analyses are chosen by sliding a window along the consensus gestalt. Each new window must start at least jump bases from the start of the previous window.

precision

there must be at least one difference in fragment lengths among all input genomes that is at least this long for the given amplicon+enzyme combination to be considered variable enough for further PCR-RFLP examination.

num_restriction_enzymes

number of restriction enzymes used in an PCR-RFLP analysis before a single electrophoretic determination of fragment length distributions is made. This number may range from 0–3.

number_combinations_to_test

maximum number of haplotypes per combination tested in a multi-locus solution set to maximally discriminate all the input sequences. Thus, combinatorics are performed on _{number haplotypess}C_{number_combinations_to_test} total combinations.