All Classes
AlignmentMaker
ChartManager
ChiSquare
CoevolutionScoresAnalyzer
CoevolutionScoresCalculator
CoevolutionScoresPlotter
CommonStats
Config
ConfigException
CorrelationCoefficients
DataFormatException
ELSC
FastaMsaReader
FastaMsaWriter
FastaNucleicAcidMsaReader
FastaNucleicAcidSequence
FastaProteinMsaReader
FastaProteinSequence
FileDataStore
FileDownloader
InformationTheory
InterMsaFilter
IntraMsaFilter
Main
Main
MSA
MsaFilter
MsaMerger
MsaReader
MsaStats
MsaWriter
MutableDouble
MutableInteger
NewickTree
NewickTreeNode
NewickTreeReader
NewickTreeTokenizer
NewickTreeWriter
NewMethods
NucleicAcidSequence
PDBDistanceCalculator
PfamFastaNucleicAcidMsaReader
PfamFastaNucleicAcidSequence
PfamFastaProteinMsaReader
PfamFastaProteinSequence
PfamFastaSequence
PfamFormatUtil
ProteinSequence
Quartets
RDBDataStore
ResidueGrouper
SCA
Sequence
SequenceImpl
SitePairValidator
StockholmMsaReader
StockholmNucleicAcidMsaReader
StockholmProteinMsaReader
Task
TaskManager
TmhmmMsaReader
TmhmmMsaWriter
TmhmmNucleicAcidMsaReader
TmhmmProteinMsaReader
TreeSequenceWeighting
Util
WalkSequenceWeighting