ClustalParser: Libary for parsing Clustal tools output
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.
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- ClustalParser-1.1.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
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| 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, 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 2015-07-01T14:23:44Z |
| Distributions | LTSHaskell:1.3.0, Stackage:1.3.0 |
| Reverse Dependencies | 3 direct, 0 indirect [details] |
| Executables | ClustalParserTest |
| Downloads | 11669 total (15 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Last success reported on 2015-07-01 [all 1 reports] |
Readme for ClustalParser-1.1.0
[back to package description]ClustalParser 
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)