All Classes
AboutDlg
AlignColumn
AlignmentGUI
AlignmentMove
AlignmentMove
AlignmentSample
AlignmentSample
AllEdgeMove
AminoAcidModel
AutomateParameters
Benchmarks
BetaDistribution
BetaPrior
Blosum
Blosum62
CircularArray
Cluster
CNetwork
CNetworkEdge
CNetworkNode
CNetworkPath
CNetworkSplit
CNetworkView
ColorGradient
CommandLine
ComplexPair
ConfReader
ConsensusNetwork
ConsensusNetworkTester
ConsensusTreeVisualizer
ContinuousPositiveParameterMove
ContinuousPositiveStructAlignMove
CoorReader
CoreMcmcModule
CorrectnessTester
CpRev
CTMain
CTree
CurrentAlignment
CurrentTreeVisualizer
DataManager
DataReader
Dataset
DataType
Dayhoff
DisplayString
Distance
DistanceGUI
DNAScore
EdgeLengthTester
EdgeMove
Entropy
EntropyContainer
EntropyGUI
ErrorMessage
ExperimentalData
FastaReader
Felsenstein81
Felsenstein84
FileTokenReader
Funcs
GammaDistribution
GammaPrior
GammaProposal
GaussianProposal
HashEntry
HashTable
HashUtils
HelpWindow
HierarchicalContinuousPositiveStructAlignMove
HKY85
Hmm
Hmm2
HmmNonParam
HmmSilent
HmmTkf92
HorizontalCladogramTreeView
HorizontalPhylogramTreeView
HyperbolicPrior
IllegalFormatException
IndelMove
Input
InputData
InputGUI
InputReader
InverseGammaPrior
Jones
JukesCantor
Kimura3
LambdaMove
Libraries
LibraryMove
LinearLink
LinearPrior
LinkFunction
LOCALTopologyMove
LogisticProposal
LogLikelihoodTrace
LogLikelihoodTraceContainer
LogLikelihoodTraceGUI
LogNormalPrior
MainFrame
MainManager
MainThread
Mapping
Mcmc
McmcCombinationMove
McmcModule
McmcMove
MCMCPars
McmcSettingsDlg
McmcStep
ModelExtension
ModelExtManager
MpdAlignment
MPIUtils
MtMam
MtREV
MultiNormCholesky
MultiplicativeProposal
MuMove
NetworkTreeView
NewickParser
NewickParserException
NewickReader
NewickReader.FormatExceptType
NormalDistribution
NucleotideModel
NucleotideModelUtils
OutputPreferences
Pair
PairCompare
ParameterInterface
PDBReader
PhiMove
PluginParameters
Postprocess
PostprocessManager
PPFold
PPFold
PPFoldGUI
PriorDistribution
ProposalDistribution
ProteinSkeletons
QuadraticLink
RawSequences
RecognitionError
Reversed
ReversibleNucleotide
RhoMove
RMove
RmsdTrace
RNAAliFold
RNAalifold
RNAalifoldResult
RNAFoldingTools
RNASettingsDlg
RotationMove
RotationOrTranslationMove
RotationProposal
RtREV
ScrollAdapter
SilentIndelMove
SimpleStats
StatAlign
StatAlignParallel
StatAlignResult
State
Stoppable
StoppableThread
StoppedException
StructAlign
StructAlignMoveParams
StructAlignParameterInterface
StructAlignTraceGUI
StructAlignTraceParameters
StructTrace
Structure
StructureDetails
StructureGUI
SubstitutionModel
SubstitutionScore
SubstMove
Subtree
Tamura92
TamuraNei
TaxaMap
TestNetwork
TextDlg
ThetaMove
TopologyMove
Track
Transformation
TranslationMove
Tree
TreeAlgo
TreeNode
TreeView
TreeVisualizer
UniformPrior
UniformProposal
Utils
Utils
Vertex
VerticalPhylogramTreeView
VisualDistance
vonMises
vonMisesFisher
Vt
Wag