ClustalParser

Libary for parsing Clustal tools output

Version on this page:1.2.3
LTS Haskell 16.3:1.3.0
Stackage Nightly 2020-06-29:1.3.0
Latest on Hackage:1.3.0

See all snapshots ClustalParser appears in

GPL-3.0-only licensed by Florian Eggenhofer
Maintained by [email protected]

Module documentation for 1.2.3

This version can be pinned in stack with:[email protected]:1d26550c03dcfcbd7048f31f0cdd768db4840ce15133676c1ed3cb681068cc3e,2414

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)