Monthly Downloads: 36
Programming language: Haskell
License: GNU General Public License v3.0 only
Latest version: v1.3.0

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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)