File List

Here is a list of all files with brief descriptions:

Bpp/Seq/CodonSiteTools.cpp [code]
Bpp/Seq/CodonSiteTools.h [code]
Bpp/Seq/DistanceMatrix.cpp [code]
Bpp/Seq/DistanceMatrix.h [code]
Bpp/Seq/DNAToRNA.cpp [code]
Bpp/Seq/DNAToRNA.h [code]
Bpp/Seq/NucleicAcidsReplication.cpp [code]
Bpp/Seq/NucleicAcidsReplication.h [code]
Bpp/Seq/Sequence.cpp [code]
Bpp/Seq/Sequence.h [code]
Bpp/Seq/SequenceExceptions.cpp [code]
Bpp/Seq/SequenceExceptions.h [code]
Bpp/Seq/SequenceIterator.h [code]
Bpp/Seq/SequencePositionIterators.cpp [code]
Bpp/Seq/SequencePositionIterators.h [code]
Bpp/Seq/SequenceTools.cpp [code]
Bpp/Seq/SequenceTools.h [code]
Bpp/Seq/SequenceWalker.cpp [code]
Bpp/Seq/SequenceWalker.h [code]
Bpp/Seq/SequenceWithAnnotation.cpp [code]
Bpp/Seq/SequenceWithAnnotation.h [code]
Bpp/Seq/SequenceWithAnnotationTools.cpp [code]
Bpp/Seq/SequenceWithAnnotationTools.h [code]
Bpp/Seq/SequenceWithQuality.cpp [code]
Bpp/Seq/SequenceWithQuality.h [code]
Bpp/Seq/SequenceWithQualityTools.cpp [code]
Bpp/Seq/SequenceWithQualityTools.h [code]
Bpp/Seq/Site.cpp [code]
Bpp/Seq/Site.h [code]
Bpp/Seq/SiteExceptions.cpp [code]
Bpp/Seq/SiteExceptions.h [code]
Bpp/Seq/SiteIterator.h [code]
Bpp/Seq/SiteTools.cpp [code]
Bpp/Seq/SiteTools.h [code]
Bpp/Seq/StringSequenceTools.cpp [code]
Bpp/Seq/StringSequenceTools.h [code]
Bpp/Seq/SymbolList.cpp [code]
Bpp/Seq/SymbolList.h [code]
Bpp/Seq/SymbolListTools.cpp [code]
Bpp/Seq/SymbolListTools.h [code]
Bpp/Seq/Transliterator.cpp [code]
Bpp/Seq/Transliterator.h [code]
Bpp/Seq/Alphabet/AbstractAlphabet.cpp [code]
Bpp/Seq/Alphabet/AbstractAlphabet.h [code]
Bpp/Seq/Alphabet/Alphabet.h [code]
Bpp/Seq/Alphabet/AlphabetExceptions.cpp [code]
Bpp/Seq/Alphabet/AlphabetExceptions.h [code]
Bpp/Seq/Alphabet/AlphabetState.h [code]
Bpp/Seq/Alphabet/AlphabetTools.cpp [code]
Bpp/Seq/Alphabet/AlphabetTools.h [code]
Bpp/Seq/Alphabet/BinaryAlphabet.cpp [code]
Bpp/Seq/Alphabet/BinaryAlphabet.h [code]
Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp [code]
Bpp/Seq/Alphabet/CaseMaskedAlphabet.h [code]
Bpp/Seq/Alphabet/CodonAlphabet.cpp [code]
Bpp/Seq/Alphabet/CodonAlphabet.h [code]
Bpp/Seq/Alphabet/DefaultAlphabet.cpp [code]
Bpp/Seq/Alphabet/DefaultAlphabet.h [code]
Bpp/Seq/Alphabet/DNA.cpp [code]
Bpp/Seq/Alphabet/DNA.h [code]
Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.cpp [code]
Bpp/Seq/Alphabet/EchinodermMitochondrialCodonAlphabet.h [code]
Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.cpp [code]
Bpp/Seq/Alphabet/InvertebrateMitochondrialCodonAlphabet.h [code]
Bpp/Seq/Alphabet/LetterAlphabet.h [code]
Bpp/Seq/Alphabet/NucleicAlphabet.h [code]
Bpp/Seq/Alphabet/NucleicAlphabetState.h [code]
Bpp/Seq/Alphabet/ProteicAlphabet.cpp [code]
Bpp/Seq/Alphabet/ProteicAlphabet.h [code]
Bpp/Seq/Alphabet/ProteicAlphabetState.h [code]
Bpp/Seq/Alphabet/RNA.cpp [code]
Bpp/Seq/Alphabet/RNA.h [code]
Bpp/Seq/Alphabet/RNY.cpp [code]
Bpp/Seq/Alphabet/RNY.h [code]
Bpp/Seq/Alphabet/StandardCodonAlphabet.cpp [code]
Bpp/Seq/Alphabet/StandardCodonAlphabet.h [code]
Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.cpp [code]
Bpp/Seq/Alphabet/VertebrateMitochondrialCodonAlphabet.h [code]
Bpp/Seq/Alphabet/WordAlphabet.cpp [code]
Bpp/Seq/Alphabet/WordAlphabet.h [code]
Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.cpp [code]
Bpp/Seq/Alphabet/YeastMitochondrialCodonAlphabet.h [code]
Bpp/Seq/AlphabetIndex/AAChargeIndex.h [code]
Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h [code]
Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h [code]
Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h [code]
Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h [code]
Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp [code]
Bpp/Seq/AlphabetIndex/AAIndex1Entry.h [code]
Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp [code]
Bpp/Seq/AlphabetIndex/AAIndex2Entry.h [code]
Bpp/Seq/AlphabetIndex/AAMassIndex.h [code]
Bpp/Seq/AlphabetIndex/AASEA1030Index.h [code]
Bpp/Seq/AlphabetIndex/AASEAInf10Index.h [code]
Bpp/Seq/AlphabetIndex/AASEASup30Index.h [code]
Bpp/Seq/AlphabetIndex/AASurfaceIndex.h [code]
Bpp/Seq/AlphabetIndex/AAVolumeIndex.h [code]
Bpp/Seq/AlphabetIndex/AlphabetIndex1.h [code]
Bpp/Seq/AlphabetIndex/AlphabetIndex2.h [code]
Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [code]
Bpp/Seq/AlphabetIndex/BLOSUM50.h [code]
Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp [code]
Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h [code]
Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp [code]
Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h [code]
Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h [code]
Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h [code]
Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h [code]
Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp [code]
Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h [code]
Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h [code]
Bpp/Seq/AlphabetIndex/SimpleScore.cpp [code]
Bpp/Seq/AlphabetIndex/SimpleScore.h [code]
Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h [code]
Bpp/Seq/App/SequenceApplicationTools.cpp [code]
Bpp/Seq/App/SequenceApplicationTools.h [code]
Bpp/Seq/Container/AbstractSequenceContainer.cpp [code]
Bpp/Seq/Container/AbstractSequenceContainer.h [code]
Bpp/Seq/Container/AlignedSequenceContainer.cpp [code]
Bpp/Seq/Container/AlignedSequenceContainer.h [code]
Bpp/Seq/Container/CompressedVectorSiteContainer.cpp [code]
Bpp/Seq/Container/CompressedVectorSiteContainer.h [code]
Bpp/Seq/Container/MapSequenceContainer.cpp [code]
Bpp/Seq/Container/MapSequenceContainer.h [code]
Bpp/Seq/Container/OrderedSequenceContainer.h [code]
Bpp/Seq/Container/SequenceContainer.h [code]
Bpp/Seq/Container/SequenceContainerExceptions.h [code]
Bpp/Seq/Container/SequenceContainerIterator.cpp [code]
Bpp/Seq/Container/SequenceContainerIterator.h [code]
Bpp/Seq/Container/SequenceContainerTools.cpp [code]
Bpp/Seq/Container/SequenceContainerTools.h [code]
Bpp/Seq/Container/SiteContainer.h [code]
Bpp/Seq/Container/SiteContainerExceptions.cpp [code]
Bpp/Seq/Container/SiteContainerExceptions.h [code]
Bpp/Seq/Container/SiteContainerIterator.cpp [code]
Bpp/Seq/Container/SiteContainerIterator.h [code]
Bpp/Seq/Container/SiteContainerTools.cpp [code]
Bpp/Seq/Container/SiteContainerTools.h [code]
Bpp/Seq/Container/VectorSequenceContainer.cpp [code]
Bpp/Seq/Container/VectorSequenceContainer.h [code]
Bpp/Seq/Container/VectorSiteContainer.cpp [code]
Bpp/Seq/Container/VectorSiteContainer.h [code]
Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp [code]
Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h [code]
Bpp/Seq/GeneticCode/GeneticCode.cpp [code]
Bpp/Seq/GeneticCode/GeneticCode.h [code]
Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp [code]
Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h [code]
Bpp/Seq/GeneticCode/StandardGeneticCode.cpp [code]
Bpp/Seq/GeneticCode/StandardGeneticCode.h [code]
Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp [code]
Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h [code]
Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp [code]
Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h [code]
Bpp/Seq/Io/AbstractIAlignment.h [code]
Bpp/Seq/Io/AbstractISequence.h [code]
Bpp/Seq/Io/AbstractOAlignment.h [code]
Bpp/Seq/Io/AbstractOSequence.h [code]
Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp [code]
Bpp/Seq/Io/BppOAlignmentReaderFormat.h [code]
Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp [code]
Bpp/Seq/Io/BppOAlignmentWriterFormat.h [code]
Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp [code]
Bpp/Seq/Io/BppOAlphabetIndex1Format.h [code]
Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp [code]
Bpp/Seq/Io/BppOAlphabetIndex2Format.h [code]
Bpp/Seq/Io/BppOSequenceReaderFormat.cpp [code]
Bpp/Seq/Io/BppOSequenceReaderFormat.h [code]
Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp [code]
Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h [code]
Bpp/Seq/Io/BppOSequenceWriterFormat.cpp [code]
Bpp/Seq/Io/BppOSequenceWriterFormat.h [code]
Bpp/Seq/Io/Clustal.cpp [code]
Bpp/Seq/Io/Clustal.h [code]
Bpp/Seq/Io/Dcse.cpp [code]
Bpp/Seq/Io/Dcse.h [code]
Bpp/Seq/Io/Fasta.cpp [code]
Bpp/Seq/Io/Fasta.h [code]
Bpp/Seq/Io/GenBank.cpp [code]
Bpp/Seq/Io/GenBank.h [code]
Bpp/Seq/Io/IoSequence.h [code]
Bpp/Seq/Io/IoSequenceFactory.cpp [code]
Bpp/Seq/Io/IoSequenceFactory.h [code]
Bpp/Seq/Io/IoSequenceStream.h [code]
Bpp/Seq/Io/ISequence.h [code]
Bpp/Seq/Io/ISequenceStream.h [code]
Bpp/Seq/Io/Mase.cpp [code]
Bpp/Seq/Io/Mase.h [code]
Bpp/Seq/Io/MaseTools.cpp [code]
Bpp/Seq/Io/MaseTools.h [code]
Bpp/Seq/Io/NexusIoSequence.cpp [code]
Bpp/Seq/Io/NexusIoSequence.h [code]
Bpp/Seq/Io/NexusTools.cpp [code]
Bpp/Seq/Io/NexusTools.h [code]
Bpp/Seq/Io/OSequence.h [code]
Bpp/Seq/Io/OSequenceStream.h [code]
Bpp/Seq/Io/PhredPhd.cpp [code]
Bpp/Seq/Io/PhredPhd.h [code]
Bpp/Seq/Io/PhredPoly.cpp [code]
Bpp/Seq/Io/PhredPoly.h [code]
Bpp/Seq/Io/Phylip.cpp [code]
Bpp/Seq/Io/Phylip.h [code]
Bpp/Seq/Io/SequenceFileIndex.h [code]
Bpp/Seq/Io/Stockholm.cpp [code]
Bpp/Seq/Io/Stockholm.h [code]
Bpp/Seq/Io/StreamSequenceIterator.cpp [code]
Bpp/Seq/Io/StreamSequenceIterator.h [code]