AAAlignment-class       "AAAlignment" result of pairwise sequence
                        alignment.
AAAlphabet-class        Class "AAAlphabet" Amino Acid Alphabet
AASequence              AASequence constructor
AASequence-class        "AASequence" Object representation of a
                        protein Sequence
AASequenceList-class    Class "AASequenceList" - Container
EPAM110                 Amino Acid Substitution matrices
Submatrix-class         Class "Submatrix" Substitution Matrix
listdist-methods        Compute distance matrix from a list
readFasta-methods       reader for databases in Fasta file format.
salign-methods          Optimal pairwise alignment of two protein
                        sequences.
sequlist                AASequenceList with 66 entries.
testalign-methods       Scoring of optimal alingments.
