bio-0.5.2: A bioinformatics library

# bio-0.5.2: 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

- Bio
  - Alignment
    - 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
  - GFF3
    - Bio.GFF3.Escape
    - Bio.GFF3.Feature
    - Bio.GFF3.FeatureHier
    - Bio.GFF3.FeatureHierSequences
    - Bio.GFF3.SGD
  - Location
    - Bio.Location.ContigLocation
    - Bio.Location.LocMap
    - Bio.Location.Location
    - Bio.Location.OnSeq
    - Bio.Location.Position
    - Bio.Location.SeqLocMap
    - Bio.Location.SeqLocation
    - Bio.Location.Strand
  - Bio.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
  - Bio.Util
    - Bio.Util.Parsex