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| .callPerl | Assistant Functions |
| .onLoad | Load packages and data |
| .pathPerl | Assistant Functions |
| aa.index | Assistant Functions |
| aaClass | Assistant Functions |
| aligndisHR | Homolog Reduction |
| basic | Assistant Functions |
| cdhitHR | Homolog Reduction |
| classify | Classification with Specific Features and Cross-Validation |
| classifyModelBAG | Classification Models |
| classifyModelCTREE | Classification Models |
| classifyModelCTREELIBSVM | Classification Models |
| classifyModelKNN | Classification Models |
| classifyModelLIBSVM | Classification Models |
| classifyModelNB | Classification Models |
| classifyModelNNET | Classification Models |
| classifyModelRF | Classification Models |
| classifyModelRPART | Classification Models |
| classifyModelSVMLIGHT | Classification Models |
| classifyModelTree | Classification Models |
| DiProDB | Assistant Functions |
| distance | Homolog Reduction |
| dssp.ss | Assistant Functions |
| elements | Assistant Functions |
| featureAAindex | Feature Coding by physicochemical/biochemical properties in AAindex |
| featureACF | Feature Coding by physicochemical/biochemical properties in AAindex |
| featureACH | Feature Coding by hydrophobicity |
| featureACI | Feature Coding by physicochemical/biochemical properties in AAindex |
| featureBDNAVIDEO | Feature Coding by DNA/RNA property |
| featureBinary | Feature Coding by Binary Vectors |
| featureCKSAAP | Feature Coding by k-spaced Aminoacids/Base Pairs |
| featureCTD | Feature Coding by composition, transition and distribution |
| featureDIPRODB | Feature Coding by Dinucleotide Property |
| featureDOMAIN | Feature Coding by doamin organization |
| featureEvaluate | Evaluate Different Feature Coding Schemas |
| featureFragmentComposition | Feature Coding by the composition of k-mer fragments |
| featureGapPairComposition | Feature Coding by g-spaced aminoacids/bases pairs |
| featureHydro | Feature Coding by hydrophobicity |
| featurePseudoAAComp | Feature Coding by Pseudo Amino Acid Composiion |
| featurePSSM | Feature Coding |
| featureSSC | Feature Coding by secondary structure |
| getDSSP | Feature Coding by secondary structure |
| getNegSite | Homolog Reduction |
| getTrain | Homolog Reduction |
| hr | Homolog Reduction |
| model | Classification Models |
| performance | Performance Evaluation |
| predictPFAM | Feature Coding by doamin organization |
| predictPROTEUS | Feature Coding by secondary structure |
| PROPERTY | Assistant Functions |
| pwm | Assistant Functions |
| selectFFS | feature forward selection |
| selectWeka | Feature Selection by Weka |
| sub.seq | Assistant Functions |