No. It is not trivial to convert either. Pregap was written in Unix bourne shell, whilst Pregap4 is Tcl/Tk.
Preferably run it on the gel along with the other samples. If this is not possible, then simply designate any other sample as the wild type and compare against that.
It is also possible to get Gap4 to produce a consensus trace. This requires using Pregap4 twice. Firstly process the sequences through Pregap4 will all the appropriate options except with the mutation detection module disabled. Assemble these sequences into Gap4. Within Gap4, for each contig start up the Contig Editor and select Save Consensus Trace from the command menu. This will produce a trace which is the average of the traces in that contig. Then delete the Gap4 database and reprocess the sequences using Pregap4, this time using mutation detection to compare against the consensus trace.
The next step is to assemble (if not already done) and edit the sequences using Gap4. See section Introduction to Gap4.