BioSeq

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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

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