ClustalParser: Libary for parsing Clustal tools output

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

Currently contains parsers and datatypes for: clustalw2, clustalo

For more information on clustal Tools refer to http://www.clustal.org/

ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences.

Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.


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Versions [faq] 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, 1.2.2, 1.2.3
Change log changelog
Dependencies base (>=4.5 && <5), ClustalParser, cmdargs, parsec [details]
License LicenseRef-GPL
Author Florian Eggenhofer
Maintainer egg@tbi.univie.ac.at
Category Bioinformatics
Source repo head: git clone https://github.com/eggzilla/ClustalParser
this: git clone https://github.com/eggzilla/ClustalParser/tree/1.0.3(tag 1.0.3)
Uploaded by FlorianEggenhofer at Tue Apr 21 09:01:31 UTC 2015
Distributions NixOS:1.2.3
Executables ClustalParserTest
Downloads 4796 total (149 in the last 30 days)
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Status Hackage Matrix CI
Docs available [build log]
Last success reported on 2015-04-21 [all 1 reports]

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Readme for ClustalParser-1.0.3

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ClustalParser Build Status

Currently contains parsers and datatypes for: clustalw2, clustalo

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