Package org.forester.phylogenyinference

Interface Summary

CharacterStateMatrix<S>
DistanceMatrix
DistanceMatrixParser
DistanceMethod

Class Summary

BasicCharacterStateMatrix<S>
BasicSymmetricalDistanceMatrix
DiscreteState
DolloParsimony
FitchParsimony<STATE_TYPE>
NeighborJoining
SankoffParsimony<STATE_TYPE>
SymmetricalDistanceMatrixParser
TestPhylogenyReconstruction

Enum Summary

CharacterStateMatrix.BinaryStates	It is crucial that the order ABSENT, UNKNOWN, PRESENT not be changes since this determines the sort order.
CharacterStateMatrix.Format
CharacterStateMatrix.GainLossStates
CharacterStateMatrix.NucleotideStates
DistanceMatrix.Format
SymmetricalDistanceMatrixParser.InputMatrixType