h$:2      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~                                                                                        Character interface(c) Dominik Schrempf 2018GPL-3.0-or-laterdominik.schrempf@gmail.comunstableportableNone U elynx-seq7IUPAC characters with a mapping to extended characters. elynx-seq2An extended character type with gaps and unknowns. elynx-seqA set of characters forms an . At the moment,  is used, since none of the alphabets has more than 255 characters. elynx-seqWrite characters. elynx-seqRead characters.  elynx-seqConversion to .  elynx-seqConversion from .  elynx-seqConversion to .  elynx-seqConversion from .  elynx-seq"Is the character a gap or unknown? elynx-seqCheck if a IUPAC & is unknown (e.g., N for nucleotides). elynx-seq)Is the given character a IUPAC character? elynx-seq,Is the given character a standard character? elynx-seq3Convert between character classes. May throw error.   &Amino acid related types and functions(c) Dominik Schrempf 2018GPL-3.0-or-laterdominik.schrempf@gmail.comunstableportableNone > elynx-seq Amino acids.!" #$%&'!" #$%&'&Amino acid related types and functions(c) Dominik Schrempf 2018GPL-3.0-or-laterdominik.schrempf@gmail.comunstableportableNone /3 elynx-seq Amino acids.3=B65CAD;7@HE>?489:?489:?@ABCDEFGHIJK,-./0123456789:;<=>L?MNOPQRSTUVWX,-./0123456789:;<=>YZ[\L?]^_`abcdefghi,-./0123456789:;<=>jklmnopqrs !"#$%tuvwxyz{|}~~&'(  , - 1 ;            , - 1 ;  =  6 4 : > Z . 2 < 7 ?              , - 1 ; ?                                     &elynx-seq-0.5.0-IODIDeq3HgtHUSu0VJRMkpELynx.Data.Character.CharacterELynx.Data.Character.AminoAcidXELynx.Data.Character.AminoAcidSELynx.Data.Character.AminoAcidIELynx.Data.Character.AminoAcidELynx.Data.Alphabet.CharacterELynx.Data.Alphabet.Alphabet)ELynx.Data.Alphabet.DistributionDiversityELynx.Data.Character.Nucleotide ELynx.Data.Character.NucleotideI ELynx.Data.Character.NucleotideXELynx.Data.Character.CodonELynx.Data.Sequence.DefaultsELynx.Data.Sequence.SequenceELynx.Data.Sequence.DistanceELynx.Data.Sequence.AlignmentELynx.Data.Sequence.TranslateELynx.Export.Sequence.FastaELynx.Import.Sequence.FastaELynx.Data.AlphabetAlphabetSsummarizeSequenceListPaths_elynx_seq CharacterIunknowniupac toStandard CharacterXgap CharactertoWordfromWordtoCharfromChartoString fromStringisGap isUnknownisIUPAC isStandardconvert AminoAcidXACDEFGHIKLMNPQRTVWYGap$fShowAminoAcidX$fReadAminoAcidX$fEqAminoAcidX$fOrdAminoAcidX$fEnumAminoAcidX$fBoundedAminoAcidX$fCharacterXAminoAcidX$fCharacterAminoAcidX$fVectorVectorAminoAcidX$fMVectorMVectorAminoAcidX$fUnboxAminoAcidX AminoAcidSStop$fShowAminoAcidS$fReadAminoAcidS$fEqAminoAcidS$fOrdAminoAcidS$fEnumAminoAcidS$fBoundedAminoAcidS$fCharacterXAminoAcidS$fCharacterAminoAcidS$fVectorVectorAminoAcidS$fMVectorMVectorAminoAcidS$fUnboxAminoAcidS AminoAcidIJBZX$fShowAminoAcidI$fReadAminoAcidI$fEqAminoAcidI$fOrdAminoAcidI$fEnumAminoAcidI$fBoundedAminoAcidI$fCharacterIAminoAcidI$fCharacterXAminoAcidI$fCharacterAminoAcidI$fVectorVectorAminoAcidI$fMVectorMVectorAminoAcidI$fUnboxAminoAcidI AminoAcid$fShowAminoAcid$fReadAminoAcid $fEqAminoAcid$fOrdAminoAcid$fEnumAminoAcid$fBoundedAminoAcid$fCharacterAminoAcid$fVectorVectorAminoAcid$fMVectorMVectorAminoAcid$fUnboxAminoAcidtoCVecfromCVec$fReadCharacter$fShowCharacter $fEqCharacter$fOrdCharacter$fBoundedCharacter$fVectorVectorCharacter$fMVectorMVectorCharacter$fUnboxCharacter AlphabetSpecstdalltoStdDNADNAXDNAIProteinProteinXProteinSProteinIalphabetDescription alphabetSpecisStdisMember$fToJSONAlphabet$fFromJSONAlphabet$fShowAlphabet$fReadAlphabet $fEqAlphabet $fOrdAlphabet$fEnumAlphabet$fBoundedAlphabet$fGenericAlphabetentropy kEffEntropy homoplasy kEffHomoplasyfrequencyCharacters Nucleotide$fShowNucleotide$fReadNucleotide$fEqNucleotide$fOrdNucleotide$fEnumNucleotide$fBoundedNucleotide$fCharacterNucleotide$fVectorVectorNucleotide$fMVectorMVectorNucleotide$fUnboxNucleotide NucleotideIU$fShowNucleotideI$fReadNucleotideI$fEqNucleotideI$fOrdNucleotideI$fEnumNucleotideI$fBoundedNucleotideI$fCharacterINucleotideI$fCharacterXNucleotideI$fCharacterNucleotideI$fVectorVectorNucleotideI$fMVectorMVectorNucleotideI$fUnboxNucleotideI NucleotideX$fShowNucleotideX$fReadNucleotideX$fEqNucleotideX$fOrdNucleotideX$fEnumNucleotideX$fBoundedNucleotideX$fCharacterXNucleotideX$fCharacterNucleotideX$fVectorVectorNucleotideX$fMVectorMVectorNucleotideX$fUnboxNucleotideX UniversalCodeStandardVertebrateMitochondrialCodon fromVecUnsafe translate translateX translateI$fToJSONUniversalCode$fFromJSONUniversalCode$fShowUniversalCode$fReadUniversalCode$fEqUniversalCode$fOrdUniversalCode$fEnumUniversalCode$fBoundedUniversalCode$fGenericUniversalCode $fShowCodon $fReadCodon $fEqCodon $fOrdCodon nameWidth summaryLengthsummaryNSequences fieldWidthSequencename descriptionalphabet characters Characters DescriptionNamefromByteString toByteString summarizesummarizeSequencesheaderbodylength equalLengthlongesttrimconcatconcatSequencesfilterShorterThanfilterLongerThanfilterStandard$fShowSequence $fEqSequencehamming FrequencyData Alignmentnames descriptionsmatrix nSequences fromSequences toSequencesjoinconcatAlignmentsfilterColsConstantfilterColsConstantSoftfilterColsOnlyStd filterColsStdfilterColsNoGapstoFrequencyData distributioncountIUPACChars countGaps countUnknowns subSamplerandomSubSample$fShowAlignment $fEqAlignment translateSeqsequenceToFastasequencesToFasta fastaSequencefastabaseGHC.WordWord8ghc-prim GHC.TypesCharGHC.BaseStringcontainers-0.6.2.1Data.Set.InternalSetbytestring-0.10.10.0Data.ByteString.Lazy.Internal ByteStringversion getBinDir getLibDir getDynLibDir getDataDir getLibexecDir getSysconfDirgetDataFileName