To run the sh2.seq scan but with the NALL algorithm we can type:
scanps -ssh2.seq -a1 -F1 -l40 -n > sh2.all.scan Minimum score set to: 63.000000 Length: 40 Probability: 0.000100 Grand Total of Paths Considered: 237
The new arguments to scanps are -l40 which specifies a minimum length of 40 for alignments and -n which stops the -a1 option from displaying alignments. The default probability cutoff is set in the SCANPSDEFAULTS file, but may be overridden by the -g command line option. For example:
scanps -ssh2.seq -a1 -g0.000001 -F1 -l40 -n Minimum score set to: 79.000000 Length: 40 Probability: 0.000001
Note that with the smaller probability threshold, the minimum score that will be considered has increased from 63 to 79. This will reduce the scan time.
The scan with default probability threshold, again on the PIR38 database, takes 877 seconds on the Indy R4000 SC. The scan considered 237 alignments to be within the probability threshold.