Align the sequences in:

multi-fasta file   sample file
against the optical map in   sample file
where the restriction site was   for e.g. CTTAAG for AflII
Note: For a typical bacterial genome we find that ~80% of the genome can be scaffolded with a single map. If your results are much worse, it is possibly due to a bug or incorrect use of the software. Please do not hesitate to contact us if you find such an instance. Also, a script to merge results from multiple optical maps will soon be available and it is likely to improve results further if multiple maps are available.

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