Popularity
3.0
Declining
Activity
0.0
Stable
4
2
0

Monthly Downloads: 77
Programming language: Haskell
License: GNU General Public License v3.0 only
Latest version: v1.3.0

ClustalParser alternatives and similar packages

Based on the "Bioinformatics" category.
Alternatively, view ClustalParser alternatives based on common mentions on social networks and blogs.

Do you think we are missing an alternative of ClustalParser or a related project?

Add another 'Bioinformatics' Package

README

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)