Alphabet                built alphabet
DLData                  Create 'DLData' object
alphabet.dna            DNA alphabet
alphabet.dna.gap        DNA alphabet with gaps
alphabet.protein        Amino acid alphabet
alphabet.protein.gap    Amino acid alphabet with gaps
alphabet.rna            RNA alphabet
alphabet.rna.gap        RNA alphabet with gaps
colorchart              Plot a colorchart representation of a set of
                        sequences.
deprects                Rectangles of averaged colors
filter.by.conservation
                        Filter columns (sequence positions) by
                        conservation
filter.by.dependencies
                        Filter columns (sequence positions) by
                        dependency
filter.by.gaps          Filter columns (sequence positions) by gaps
filterColumns           Filter data columns by some filter function
getDeps                 Compute dependencies between positions
getPWM                  Position weight matrix from DLData object
logo                    Sequence logo
partition               Parition data by most inter-dependent positions
plotBlocks              Plots blocks of data
plotDeparcs             Plot a graph representation of dependency
                        values.
plotDeplogo             Plot a dependency logo
plotDepmatrix           Plot a matrix representation of dependency
                        values.
replaceColors           Replace colors in DLData object
revcom                  Reverse complement
subBoxes                Plot weights as boxplots
subLines                Plot weights as lines
suggestColors           Suggest colors for symbols
summary.DLData          Summarizing DLData objects
