The ClustalParser package

[ Tags: bioinformatics, gpl, library, program ] [ Propose Tags ]

Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign

Clustal tools are multiple sequence alignment tools for biological sequence like DNA, RNA and Protein. For more information on clustal Tools refer to http://www.clustal.org/.

Mlocarna is a multiple sequence alignment tool for RNA sequences with secondary structure output. For more information on mlocarna refer to http://www.bioinf.uni-freiburg.de/Software/LocARNA/.

Cmalign is a multiple sequence alignment program based on RNA family models and produces ,among others, clustal output. It is part of infernal http://infernal.janelia.org/.


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Versions 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.2.0, 1.2.1
Change log changelog
Dependencies base (>=4.5 && <5), ClustalParser, cmdargs, either-unwrap, parsec (>=3.1.9), text, vector [details]
License GPL-3.0
Author Florian Eggenhofer
Maintainer egg@tbi.univie.ac.at
Category Bioinformatics
Source repository head: git clone https://github.com/eggzilla/ClustalParser
this: git clone https://github.com/eggzilla/ClustalParser/tree/1.2.1(tag 1.2.1)
Uploaded Mon Feb 6 18:34:36 UTC 2017 by FlorianEggenhofer
Distributions LTSHaskell:1.2.1, NixOS:1.2.1, Stackage:1.2.1, Tumbleweed:1.2.1
Executables ClustalParserTest
Downloads 2284 total (396 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2017-02-06 [all 1 reports]
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Readme for ClustalParser-1.2.1

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ClustalParser Hackage Build Status

Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign

Clustal tools are multiple sequence alignment tools for biological sequences like DNA, RNA and Protein. For more information on clustal Tools refer to http://www.clustal.org/.

Mlocarna is a multiple sequence alignment tool for RNA sequences with secondary structure output. For more information on mlocarna refer to http://www.bioinf.uni-freiburg.de/Software/LocARNA/.

cmalign is a multiple sequence alignment program based on RNA family models and produces ,among others, clustal output. It is part of infernal http://infernal.janelia.org/.

4 types of output are parsed

  • Alignment file (.aln):

    • Parsing with readClustalAlignment from filepath (Bio.ClustalParser)
    • Parsing with parseClustalAlignment from String (Bio.ClustalParser)
  • Alignment file with secondary structure (.aln):

    • Parsing with readStructuralClustalAlignment from filepath (Bio.ClustalParser)
    • Parsing with parsStructuralClustalAlignment from String (Bio.ClustalParser)
  • Summary (printed to STDOUT):

    • Parsing with readClustalSummary from filepath (Bio.ClustalParser)
    • Parsing with parseClustalSummary from String (Bio.ClustalParser)
  • Phylogenetic Tree (.dnd):

    • Parsing with readGraphNewick from filepath (Bio.Phylogeny)
    • Parsing with readGraphNewick from String (Bio.Phylogeny)