bio-0.4.6: A bioinformatics libraryContentsIndex
bio-0.4.6: A bioinformatics library

This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities.

Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also Blast output parsing. Partly implemented single linkage clustering, and multiple alignment. Reading Gene Ontology (GO) annotations (GOA) and definitions/hierarchy.

The Darcs repository is at: http://malde.org/~ketil/biohaskell/biolib.

Modules
show/hideBio
show/hideAlignment
Bio.Alignment.AAlign
Bio.Alignment.ACE
Bio.Alignment.AlignData
Bio.Alignment.BED
Bio.Alignment.Blast
Bio.Alignment.BlastData
Bio.Alignment.BlastFlat
Bio.Alignment.BlastXML
Bio.Alignment.Bowtie
Bio.Alignment.Matrices
Bio.Alignment.Multiple
Bio.Alignment.PSL
Bio.Alignment.QAlign
Bio.Alignment.SAlign
Bio.Alignment.Soap
Bio.Clustering
show/hideGFF3
Bio.GFF3.Escape
Bio.GFF3.Feature
Bio.GFF3.FeatureHier
Bio.GFF3.FeatureHierSequences
Bio.GFF3.SGD
show/hideLocation
Bio.Location.ContigLocation
Bio.Location.LocMap
Bio.Location.Location
Bio.Location.OnSeq
Bio.Location.Position
Bio.Location.SeqLocMap
Bio.Location.SeqLocation
Bio.Location.Strand
show/hideBio.Sequence
Bio.Sequence.AminoProperties
Bio.Sequence.Entropy
Bio.Sequence.FastQ
Bio.Sequence.Fasta
Bio.Sequence.GOA
Bio.Sequence.GeneOntology
Bio.Sequence.HashWord
Bio.Sequence.KEGG
Bio.Sequence.Phd
Bio.Sequence.SFF
Bio.Sequence.SFF_filters
Bio.Sequence.SFF_name
Bio.Sequence.SeqData
Bio.Sequence.TwoBit
show/hideBio.Util
Bio.Util.Parsex
Bio.Util.TestBase
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