ClustalParser: Libary for parsing Clustal tools output

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

Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna

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]
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, either-unwrap, parsec (>=3.1.9), vector [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/1.1.0(tag 1.1.0)
Uploaded by FlorianEggenhofer at Wed Jul 1 14:23:44 UTC 2015
Distributions NixOS:1.2.3
Executables ClustalParserTest
Downloads 4685 total (305 in the last 30 days)
Rating (no votes yet) [estimated by rule of succession]
Your Rating
  • λ
  • λ
  • λ
Status Hackage Matrix CI
Docs available [build log]
Last success reported on 2015-07-01 [all 1 reports]

Modules

[Index]

Downloads

Maintainer's Corner

For package maintainers and hackage trustees


Readme for ClustalParser-1.1.0

[back to package description]

ClustalParser Hackage Build Status

Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna

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 molocarna 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)