addCon                  Add constraints to an already existing
                        constraint set
align-class             Class "align"
bfile2tmat              Converting a MEME-style background file to a
                        transition matrix
bgModel                 Estimating the background Markov model
boundCon-class          Class "boundCon"
constraintSet-class     Class "constraintSet" ~~~
cosmo                   Constrained motif detection main function
cosmo-class             Class "cosmo"
intInfo-class           Class "intInfo" ~~~
license.cosmo           Print cosmo license
makeBoundCon            Constructing a bound constraint
makeConSet              Constructing a constraint set.
makePalCon              Constructing a palindromic constraint
makePosFreqCon          Constructing a nucleotide frequency constraint
makeShapeCon            Constructing a shape constraint
makeShapeDiffCon        Constructing a shape parameter difference
                        constraint
makeSubMotifCon         Constructing a submotif constraint
motifPWM                Example position weight matrix
palCon-class            Class "palCon"
posFreqCon-class        Class "posFreqCon" ~~~
postProbs-class         Class "postProbs"
readConFile             Reads in a constraint file.
rseq                    Random generation of DNA sequence according to
                        ZOOPS or TCM model
shapeCon-class          Class "shapeCon"
shapeDiffCon-class      Class "shapeDiffCon" ~~~
simScore                Score motif detection simulation results
subMotifCon-class       Class "subMotifCon" ~~~
transMats               Example transition matrix in list format
writeConFile            Converts an object of class 'constraintSet'
                        into a text file
