Interface Summary Interface Description AAIndexProvider
Class Summary Class Description AAindexFactoryFactory class to get Providers for substitution matrices that are provided by the AAINDEX database. AAIndexFileParser DefaultAAIndexProviderThe default provider for AAINDEX loads substitution matrices from the AAINDEX file in the resources directory ScaledSubstitutionMatrixThe biojava-alignment module represents substitution matrices with short values. SimpleSubstitutionMatrix<C extends Compound>Implements a data structure which holds the score (penalty or bonus) given during alignment for the exchange of one
Compoundin a sequence for another.
SubstitutionMatrixHelperStatic utility to access substitution matrices that come bundled with BioJava.