It allows you to access most of hmmemit's parameters from the GCG command line. These are output in a single RSF file, and can be output as is, or with gaps inserted as necessary so that they are in alignment with each other. Creating temp file for input to hmmemit.
LineUp is a multiple sequence editor used to create multiple sequence alignments.
Pretty displays multiple sequence alignments. ProfileMake makes a profile from a multiple sequence alignment. ProfileSearch uses the profile to search a database for sequences with similarity to the group of aligned sequences. ProfileGap makes optimal alignments between one or more sequences and a group of aligned sequences represented as a profile. ProfileScan finds structural and sequence motifs in protein sequences, using predetermined parameters to determine significance.