Hackage :: [Package]

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.

[Skip to Readme]

Downloads

Maintainer's Corner

Package maintainers

For package maintainers and hackage trustees

Candidates

Versions [RSS] 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, 1.3.0
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 2015-04-21T09:01:31Z
Distributions LTSHaskell:1.3.0, Stackage:1.3.0
Reverse Dependencies 3 direct, 0 indirect [details]
Executables ClustalParserTest
Downloads 11221 total (36 in the last 30 days)
Rating (no votes yet) [estimated by Bayesian average]
Your Rating
  • λ
  • λ
  • λ
Status Docs available [build log]
Last success reported on 2015-04-21 [all 1 reports]

Readme for ClustalParser-1.0.3

[back to package description]

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)