Minimal Syntax: % gelmerge -Default
Prompted Parameters:
-WORdsize=7           sets word size for overlap determination
-STRIngency=0.8       sets minimum fraction of matching words in overlap
-MINOverlap=14        sets minimum length of overlap
Local Data Files:
-MATRix1=gelmergedna.cmp       assigns the scoring matrix for contig assembly
-MATRix2=gelmergelocaldna.cmp  assigns the scoring matrix for vector recognition
Optional Parameters:
-MINIdentity=14         sets minimum run of identical bases found at least
                          once in an overlap between two contigs
-MAXGap=10              sets maximum gap size for overlap determination
-GAPweight=8            sets gap creation penalty in contig assembly
-LENgthweight=2         sets gap extension penalty in contig assembly
-ARChive                creates contigs from the original gel readings
-WORKing                creates contigs from individual working
                          fragment (with gaps removed)
-REPortfile[=Filename]  writes report of recognized vector sequences
-EXCise                 removes vector sequences from single-fragment
                          contigs
-VECTORSTrigency=0.8    sets minimum fraction of matches in vector recognition
-VECTORMINIdentity=12   sets minimum run of identical bases found at least
                          once in a match between vector and fragment
-VECTORMAXGap=5         sets maximum gap size in first step of vector
                          recognition
-VECTORGAPweight=30     sets gap creation penalty in vector recognition
-VECTORLENgthweight=3   sets gap extension penalty in vector recognition
-NOMERge                suppresses contig assembly
-NOMONitor              suppresses screen trace of program progress
-NOSUMmary              suppresses screen summary at the end of the
                          program
-BATch                  submits program to the batch queue