The programs, developed at EMBL and other European bioinformatics labs include a large number of programs that are not available in GCG, or improve on existing GCG programs. You can define the patterns ambiguously and allow mismatches. You can provide the patterns in a file or simply type them in from the terminal. The output is a series of files called r1.rfind, r2.rfind, and so on, each containing a single extracted sequence. These can be fed through Pileup or manipulated in other ways.
Homologies makes a table of the pair-wise distances within a group of aligned sequences.
ToPhylip writes GCG sequences into a single file in Phylip format. GelStatus reads a GCG Fragment Assembly database, and produces a summary report of the quality of each contig. GelPicture reads a contig from the Fragment Assembly database and displays a diagram of the gel alignments and a printout of the aligned gel sequences and consensus. GelFigure produces a graphical report of the status of a contig in a fragment assembly project. MapSelect selects restriction enzymes by name or by their ability to cut a given sequence, and writes them to a new enzyme file for use in other programs.