• ClusterMakerFactory : MSTClusterMaker , TransMSTClusterMaker , PMSTClusterMaker
• ESTAnalyzerFactory : CLU , TwoPassD2 , MatrixFileAnalyzer , FMWSCA , D2Zim , D2
• FilterFactory : LCFilter , LengthFilter
• HeuristicFactory : NewUVHeuristic , UVSampleHeuristic , TVHeuristic
• operator<< : arg_parser , MSTNode , MSTCluster , MST
• ParameterSetManager : ParameterSet
• TransMSTClusterMaker : TransCacheEntry