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              Plots a colorchart representation of a set of
                        sequences
deprects                Rectangles of averaged colors
filter.by.conservation
                        Filters columns (sequence positions) by
                        conservation
filter.by.dependencies
                        Filters columns (sequence positions) by
                        dependency
filter.by.gaps          Filters columns (sequence positions) by gaps
filterColumns           Filters data columns by some filter function
getDeps                 Compute dependencies between positions
getPWM                  Position weight matrix from DLData object
logo                    Sequence logo
partition               Paritions data by most inter-dependent
                        positions
plotBlocks              Plots blocks of data
plotDeparcs             Plots a graph representation of dependency
                        values
plotDeplogo             Plot a dependency logo
plotDepmatrix           Plots a matrix representation of dependency
                        values
replaceColors           Replaces colors in DLData object
revcom                  Reverse complement
subBoxes                Plots weights as boxplots
subLines                Plots weights as lines
suggestColors           Suggests colors for symbols
summary.DLData          Summarizing DLData objects
