You also can specify a threshold value with the command-line qualifier -THReshold. This can be important in amino acid sequence analysis. The default value for the threshold qualifier is 1.0, which means that all matched residue pairs in the scoring matrix that have a value of 1.0 or greater will vote as a block in calculating a consensus residue for a particular position. If you do not want to see block voting, you can increase the threshold value with the command-line qualifier -THReshold=1.5. (1.5 is the value assigned for an identical match in the default scoring matrix used by Pretty. For example, an alanine to alanine match would be assigned a value of 1.5.) If you are using a scoring matrix other than the default one, you can use the command line qualifier -IDEntity to eliminate block voting.
Question/response taken from GCG Newsletter, March 94..