Name: bio Version: 0.3.5 License: LGPL License-file: LICENSE Author: Ketil Malde Maintainer: ketil@ii.uib.no Category: Bioinformatics Synopsis: A bioinformatics library Description: This is a collection of data structures and algorithms I've found useful when building various bioinformatics-related tools and utilities. . Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them, quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats. Rudimentary support for doing alignments - including dynamic adjustment of scores based on sequence quality - and 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: . Homepage: http://blog.malde.org/index.php/the-haskell-bioinformatics-library/ Tested-With: GHC==6.8.2 Build-Type: Simple Build-Depends: base>3, QuickCheck<2, binary, tagsoup>=0.4, bytestring >= 0.9.1, containers, array, parallel, parsec, random, old-time, mtl -- add fps for ghc 6.4.2; change imports in Bio/Sequence/TwoBit.hs if you want QC 2 -- We omit the debian/ and Test/ files because those are for development, not installation. Data-Files: README Exposed-modules: Bio.Sequence, Bio.Sequence.SeqData, Bio.Sequence.SequenceReader, Bio.Sequence.Fasta, Bio.Sequence.FastQ, Bio.Sequence.TwoBit, Bio.Sequence.Phd, Bio.Sequence.Entropy, Bio.Sequence.HashWord, Bio.Sequence.GOA, Bio.Sequence.GeneOntology, Bio.Sequence.KEGG, Bio.Sequence.SFF, Bio.Sequence.SFF_name Bio.Alignment.BlastData, Bio.Alignment.BlastFlat, Bio.Alignment.Blast, Bio.Alignment.BlastXML, Bio.Alignment.AlignData, Bio.Alignment.Matrices, Bio.Alignment.SAlign, Bio.Alignment.AAlign, Bio.Alignment.QAlign Bio.Alignment.Multiple, Bio.Alignment.ACE, Bio.Alignment.Bowtie, Bio.Alignment.Soap, Bio.Clustering, Bio.Util, Bio.Util.Parsex, Bio.Util.TestBase, Bio.Util.Parsing, Bio.Location.Display, Bio.Location.Strand, Bio.Location.Position, Bio.Location.ContigLocation, Bio.Location.Location, Bio.Location.LocMap, Bio.Location.OnSeq, Bio.Location.SeqLocation, Bio.Location.SeqLocMap, Bio.GFF3.Escape, Bio.GFF3.Feature, Bio.GFF3.FeatureHier, Bio.GFF3.GFF -- Bio.GFF3.SGD extensions: CPP, ParallelListComp ghc-options: -Wall -O2 -fexcess-precision -funbox-strict-fields -auto-all