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| Alphabet | built alphabet |
| ASN | ASN alphabet |
| createDiffLogoObject | DiffLogo object |
| differenceOfICs | normalized information content differences |
| diffLogo | Draw DiffLogo |
| diffLogoFromPwm | Draw DiffLogo from PWM |
| diffLogoTable | Draw DiffLogo-table |
| DNA | DNA alphabet |
| getPwmFromAlignment | Create PWM from alignment |
| informationContent | information content |
| lossOfAbsICDifferences | the change of information content |
| normalizedDifferenceOfProbabilities | normalized probability differences |
| probabilities | probabilities |
| RNA | RNA alphabet |
| seqLogo | Draw sequence logo |
| shannonDivergence | shannon divergence |
| sumOfAbsICDifferences | sum of absolute information content differences |
| sumOfAbsProbabilityDifferences | sum of absolute probability differences |
| sumProbabilities | sum of probabilities, i.e. 1.0 |