All Classes
aa
aaa
AbstractRenderer
Accession
Accession.Source
AccessionParser
AdjactantDirectedBinaryDomainCombination
AdjactantDirectedCombinableDomains
AncestralTaxonomyInference
AncestralTaxonomyInferenceException
AncestralTaxonomyInferrer
Annotation
AnnotationParser
annotator
AptxUtil
AptxUtil.GraphicsExportType
Archaeopteryx
ArchaeopteryxA
ArchaeopteryxE
AsciiHistogram
BasicBinaryDomainCombination
BasicCharacterStateMatrix
BasicCombinableDomains
BasicDescriptiveStatistics
BasicDomain
BasicDomainSimilarityCalculator
BasicExternalNodeBasedCoverageExtender
BasicGenomeWideCombinableDomains
BasicGoRelationship
BasicGoSubset
BasicGoTerm
BasicGoXRef
BasicMsa
BasicPhylogeniesWebserviceClient
BasicProtein
BasicSequence
BasicSpecies
BasicSymmetricalDistanceMatrix
BasicTable
BasicTableParser
BinaryCharacters
BinaryCharactersParser
BinaryDomainCombination
BinaryDomainCombination.DomainCombinationType
BinaryDomainCombination.OutputFormat
Blast
BootstrapResampler
BranchColor
BranchCountingBasedScoringMethod
BranchData
BranchLengthBasedScoringMethod
BranchWidth
BranchWidthParser
CharacterStateMatrix
CharacterStateMatrix.BinaryStates
CharacterStateMatrix.Format
CharacterStateMatrix.GainLossStates
CharacterStateMatrix.NucleotideStates
Chart
check_fasta
ClustalOmega
ColorParser
CombinableDomains
CombinationsBasedPairwiseDomainSimilarity
CombinationsBasedPairwiseDomainSimilarityCalculator
CommandLineArguments
CommandProcessBuilder
confadd
Confidence
ConfidenceAssessor
ConfidenceParser
Configuration
Configuration.EXT_NODE_DATA_RETURN_ON
Configuration.UI
Constants
core_chars
count_support
CountsBasedPairwiseDomainSimilarity
Coverage
CoverageCalculationMethod
CoverageCalculationOptions
CoverageCalculator
CoverageExtender
Date
DateParser
decorator
decoratorX
DeleteableMsa
DescriptiveStatistics
DevelopmentTools
DirectedBinaryDomainCombination
DirectedCombinableDomains
DistanceMatrix
DistanceMatrix.Format
Distribution
DistributionParser
DolloParsimony
dom_dup
Domain
DomainArchitecture
DomainArchitectureBasedGenomeSimilarityCalculator
DomainArchitectureParser
DomainCountsBasedPairwiseSimilarityCalculator
DomainCountsDifferenceUtil
DomainCountsDifferenceUtil.COPY_CALCULATION_MODE
DomainLengths
DomainLengthsTable
domainloss_replacement
DomainParsimonyCalculator
DomainSimilarity
DomainSimilarity.DomainSimilarityScoring
DomainSimilarity.DomainSimilaritySortField
DomainSimilarity.PRINT_OPTION
DomainSimilarityCalculator
DomainSimilarityCalculator.Detailedness
DomainSimilarityCalculator.GoAnnotationOutput
EasyWriter
EbiDbEntry
Event
Event.EventType
EventParser
Example1
Example2
Example3
Example4
Example5
ExternalForwardIterator
ExternalNodeBasedCoverage
ExternalNodeBasedCoverageMethod
ExternalNodeBasedCoverageMethodOptions
ExternalProgram
FailedConditionCheckException
fasta_split
FastaParser
FitchParsimony
FontChooser
ForesterConstants
ForesterConstants.PhylogeneticTreeFormats
ForesterUtil
GapContribution
gene_tree_preprocess
GeneralMsaParser
GeneralTable
genome_counts_for_once_appearing_dcs
GenomeWideCombinableDomains
GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder
get_distances
get_genome_counts_per_char
get_loss_nodes
get_shared_chars
get_subtree_specific_chars
goac
GoId
GoNameSpace
GoNameSpace.GoNamespaceType
GoRelationship
GoRelationship.Type
GoSubset
GoSubset.Type
GoTerm
GoUtils
GoXRef
GoXRef.Type
gsdi
GSDI
GSDII
GSDIR
Hello3d
HmmerRest
HmmPfamOutputParser
HmmPfamOutputParser.FilterType
HmmPfamOutputParser.ReturnType
HmmscanPerDomainTableParser
HmmscanPerDomainTableParser.FilterType
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
HmmscanPerDomainTableParser.ReturnType
Identifier
IdentifierParser
IllegalFormatUseException
ImageLoader
InferenceManager
IntMatrix
inverted_dcs
IteratingPhylogenyParser
LevelOrderTreeIterator
LogBranchLengthBasedScoringMethod
Mafft
MainFrame
MainFrameApplet
MainFrameApplication
MainPanel
map_lengths
Mapping
MappingResults
mcc
meta_ontologizer
MetaOntologizer
ModelingUtils
MolecularSequence
MolecularSequence.TYPE
Msa
Msa.MSA_FORMAT
msa_compactor
MsaCompactor
MsaFormatException
MsaInferrer
MsaMethods
MsaProperties
MsaRenderer
MultipleUris
NeighborJoining
NeighborJoiningF
NeighborJoiningR
neTest
NexusBinaryStatesMatrixParser
NexusCharactersParser
NexusConstants
NexusFormatException
NexusPhylogeniesParser
NHXFormatException
NHXParser
NHXParser.TAXONOMY_EXTRACTION
NHXtags
nj
NodeData
NodeDataField
NodeVisualData
NodeVisualData.FontType
NodeVisualData.NodeFill
NodeVisualData.NodeShape
obo_tool
OBOparser
OBOparser.ReturnType
OntologizerResult
OntologizerResult.TYPE
Options
Options.CLADOGRAM_TYPE
Options.NODE_LABEL_DIRECTION
Options.PHYLOGENY_GRAPHICS_TYPE
PairwiseDistanceCalculator
PairwiseDistanceCalculator.PWD_DISTANCE_METHOD
PairwiseDomainSimilarity
PairwiseDomainSimilarityCalculator
PairwiseGenomeComparator
ParserBasedPhylogenyFactory
ParserUtils
PaupLogParser
pccx
pfam2go_extractor
pfam_go
pfamacc2go
pfamacc2pfamid
PfamToGoMapping
PfamToGoParser
phylo2coloredgraphics
phylo2graphics
PhylogeneticInferenceOptions
PhylogeneticInferrer
PhylogeneticInferrer.MSA_PRG
PhylogeniesWebserviceClient
Phylogeny
PhylogenyBranch
PhylogenyData
PhylogenyDataPhyloXmlParser
PhylogenyDataUtil
PhylogenyDecorator
PhylogenyDecorator.FIELD
PhylogenyFactory
PhylogenyMethods
PhylogenyMethods.DESCENDANT_SORT_PRIORITY
PhylogenyMethods.PhylogenyNodeField
PhylogenyNode
PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE
PhylogenyNodeIterator
PhylogenyParser
PhylogenyParserException
PhylogenyWriter
PhylogenyWriter.FORMAT
PhyloInferenceDialog
phylostrip
phyloxml_converter
PhyloXmlDataFormatException
PhyloXmlException
PhyloXmlHandler
PhyloXmlMapping
PhyloXmlNodeWriter
PhyloXmlParser
PhyloXmlUtil
Point
PointParser
Polygon
PolygonParser
PostOrderStackObject
PostorderTreeIterator
PreorderTreeIterator
ProcessPool
ProcessRunning
PropertiesMap
Property
Property.AppliesTo
PropertyParser
Protein
ProteinCountsBasedPairwiseDomainSimilarityCalculator
ProteinDomain
ProteinDomainParser
ProteinId
Queue
RandomThing
Reference
ReferenceParser
reinv_count
RenderableDomainArchitecture
RenderableMsaSequence
RenderablePhylogenyData
RenderableVector
ResampleableMsa
ResidueRenderer
RestUtil
rio
RIO
RIO.REROOTING
RIOException
RunnableProcess
SankoffParsimony
Sarray
ScoringMethodForExternalNode
SDI
SDIException
SDIR
SDIutil
SDIutil.ALGORITHM
SDIutil.TaxonomyComparisonBase
Sequence
SequenceAccessionTools
SequenceDatabaseEntry
SequenceDataRetriver
SequenceDbWsTools
SequenceParser
SequenceRelation
SequenceRelation.SEQUENCE_RELATION_TYPE
SequenceRelationParser
SequenceWriter
SequenceWriter.SEQ_FORMAT
set_comparator
shared_chars_in_ext_nodes
simple_node_processor
SimpleDomain
Species
Sset
StringInt
StringInt.DescendingIntComparator
subtree_feature_count
support_statistics
support_transfer
SupportCount
surfacing
SurfacingConstants
SurfacingUtil
SymmetricalDistanceMatrixParser
SymmetricalDistanceMatrixParser.InputMatrixType
SystemCommandExecutor
table2fasta
tax_code_cleaner
Taxonomy
TaxonomyColors
TaxonomyDataManager
TaxonomyParser
TaxonomyUtil
Test
Test
Test
TestGo
TestGSDI
TestPccx
TestPhylogenyReconstruction
TestRIO
TestSurfacing
Time
TolParser
TolXmlHandler
TolXmlMapping
TreeColorSet
TreeFontSet
TreePanel
TreePanelUtil
TreeSplitMatrix
TxSearch
TxSearch.RANKS
TxSearch.TAX_NAME_CLASS
TxSearch.TAX_RANK
UniProtEntry
UniProtTaxonomy
Uri
UriParser
UrlTreeReader
WabiTools
WebservicesManager
WebservicesManager.WsPhylogenyFormat
WebserviceUtil
wiki_examples
WindowsUtils
XmlElement