An algorithm for multiple sequence comparison was implemented in FORTRAN 77 for VAX/VMS in GCG-atible format. The MULTICOMP program package includes several procedures with which one query sequence can be compared simultaneously to several DNA, RNA or amino acid sequences. The same technique was also introduced for comparing propensities of secondary structural features, which can be predicted on the basis of amino acid sequences. The technique has been applied to a wide range of sequence and structural analyses.