BioSeq is a Nim library for working with biological sequence data such as DNA, RNA, and amino acids.
BioSeq Modules
- seqRecord
- Container for sequence data and associated sample id.
- alignment
- Container for sequence alignment matrix and associated sample ids.
- nucleotide
- Types and procs for working with nucleotides.
- aminoAcid
- Types and procs for working with amino acids.
- fasta
- Fasta format parsing and writing.
- phylip
- Phylip alignment format parsing and writing.
- sequence
- For working with sequences of nucleotides.
- matrix
- For working with a sequence alignment matrix.
- twoBitSequence
- Storage of nucleotides sequence as a pair of bits within a bit sequence.
Exports
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nchars, []=, cols, filterColumns, newMatrix, dim, newMatrix, Alignment, numPolymorphicSites, colCharacterCount, $, $, [], nseqs, rows, filterSamples, newAlignment, toString, stack, alleleCount, concat, rowCharacterCount, Matrix, newAlignment, alleleCount, [], gCode26, gCode14, parseChar, gCode3, gCode30, gCode29, aminoAcidChar, gCode5, gCode24, gCode10, gCode2, aminoAcidDefinition, toChar, gCode9, definition, gCode22, gCode1, GeneticCode, gCode27, gCode23, gCode12, gCode6, gCode4, gCode33, gCode25, gCode13, translateCodon, gCode31, AminoAcid, gCode21, abreviation, gCode28, aminoAcidAbreviation, gCode11, gCode16, diploidBiallelicChar, parseChar, parseChar, toChar, toDiploidBiallelic, HaploidBiallelic, toChar, DiploidBiallelic, Biallelic, haploidBiallelicChar, iterFastaStream, iterFastaFile, toFastaString, iterFastaString, toFastaString, toFastaFile, toFastaFile, FastaError, $, dim, rows, cols, newMatrix, []=, toString, newMatrix, stack, concat, Matrix, [], [], toNexusFile, toNexus, toNexusString, isAdenine, parseChar, parseChar, toDNA, rnaComplement, strictDnaByte, rnaByte, isPurine, dnaChar, toUnambiguousSet, toChar, dnaComplement, parseChar, toRNA, toDNA, dnaUnambiguousSet, diffBase, sameBase, dnaByte, complement, strictDnaChar, isPyrimidine, complement, knownBase, strictDnaComplement, toChar, isThymine, StrictDNA, byte, strictRnaChar, toUnambiguousSet, StrictRNA, isCytosine, strictRnaComplement, toChar, toChar, Nucleotide, complement, isUracil, byte, parseChar, RNA, toRNA, strictRnaByte, DNA, complement, StrictNucleotide, AnyNucleotide, rnaUnambiguousSet, isGuanine, byte, rnaChar, byte, toRNA, toDNA, [], []=, len, $, TwoBitSequence, bitSeq, newTwoBitSequence, $, SeqRecord, toCharSeq, reverseComplement, translate, reverseComplement, complement, complement, toSeq, toSeq, toString, toStructure, toStructureFile, toStructureCharStr, toStructureString, toStructureCharStr, diploidStructureChar, haploidStructureChar, iterPhylipStream, toPhylipFile, iterPhylipString, toPhylipString, toPhylip, parsePhylipStream, parsePhylipFile, PhylipFormat, iterPhylipFile, PhylipError, parsePhylipString