https://github.com/eggzilla/clustalparser

Parse output of Clustal tools
https://github.com/eggzilla/clustalparser

Last synced: 13 days ago
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Parse output of Clustal tools

• Host: GitHub
• URL: https://github.com/eggzilla/clustalparser
• Owner: eggzilla
• License: gpl-3.0
• Created: 2014-02-07T13:45:46.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2019-11-15T02:07:03.000Z (about 5 years ago)
• Last Synced: 2024-11-03T11:42:47.261Z (2 months ago)
• Language: Haskell
• Size: 67.4 KB
• Stars: 4
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog.md
  • License: LICENSE

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README

        
ClustalParser [![Hackage](https://img.shields.io/hackage/v/ClustalParser.svg)](https://hackage.haskell.org/package/ClustalParser) [![Build Status](https://travis-ci.org/eggzilla/ClustalParser.svg)](https://travis-ci.org/eggzilla/ClustalParser)

=============

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 .

Mlocarna is a multiple sequence alignment tool for RNA sequences with

secondary structure output. 

For more information on mlocarna refer to .

cmalign is a multiple sequence alignment program based on RNA family models and produces

,among others, clustal output. It is part of infernal . 

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)