AMPSequences            Antimicrobial peptide sequences
AMPSequences.response   Antimicrobial peptide sequence responses
BIC                     Bayesian Information Content
Descriptors-class       Class "Descriptors"
MetricParams-class      Class "MetricParams"
MotifModel-class        Class "MotifModel"
MotifModelSet-class     Class "MotifModelSet"
SHP2Sequences           SHP-2_N-SH2 peptide sequences
Sequences-class         Class "Sequences"
TULASequences           TULA-2_Post peptide sequences
aclust                  aclust
blosum50                BLOSUM 50 substitution matrix
blosum62                BLOSUM 62 substitution matrix
blosum90                BLOSUM 90 substitution matrix
changeClusterFormat     Change cluster format
classify                classify
default.MetricParams    Default parameters for calculating
                        sequence-sequence distances
defaultBaseMatrix       defaultBaseMatrix
read.fasta              Read in sequences in FASTA format
read.sequences          Read sequence file
simpleDescriptors       Function "simpleDescriptors"
write.fasta             Write out the sequences as a FASTA file
write.sequences         Write out the sequences as a sequence file
