Packages 
Package Description
edu.dartmouth.bglab
Provides a class to hold global constants.
edu.dartmouth.bglab.beam
Provides the top level of the algorithms for BEAM, PRISM, and SPACER, along with the command-line version of SCOPE.
edu.dartmouth.bglab.beam.web
Provides WebDriver and its associated classes as a simple API to a multi-process version of SCOPE designed for use by a web front end.
edu.dartmouth.bglab.dataImportPreparation  
edu.dartmouth.bglab.io
Provides static classes for reading and writing common objects to and from file, along with a main class for loading new organisms into SCOPE.
edu.dartmouth.bglab.model
Provides implementations of several different models for representing cis-regulatory elements, along with command-line programs for testing the accuracy of these models.
edu.dartmouth.bglab.motif
Provides classes for representing, manipulating, and comparing motifs.
edu.dartmouth.bglab.score
Provides objective functions for scoring motifs.
edu.dartmouth.bglab.search
Provides classes for finding the occurrences of motifs in biological sequences.
edu.dartmouth.bglab.test
Provides test code for the other packages, and a few other odds and ends.
edu.dartmouth.bglab.util
Provides an assortment of data structures and other utilities classes; the classes in this package perform general functions which are not directly related to biology, whereas all other packages are motif-centric.