ClustalParser: Libary for parsing Clustal tools output
Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign
Clustal tools are multiple sequence alignment tools for biological sequence 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 mlocarna refer to http://www.bioinf.uni-freiburg.de/Software/LocARNA/.
Cmalign is a multiple sequence alignment program based on RNA family models and produces ,among others, clustal output. It is part of infernal http://infernal.janelia.org/.
[Skip to Readme]
Downloads
- ClustalParser-1.3.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
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.md |
| Dependencies | base (>=4.5 && <5), ClustalParser, cmdargs, either-unwrap, parsec (>=3.1.9), text, vector [details] |
| Tested with | ghc ==8.4.4, ghc ==8.6.5, ghc ==8.8.1 |
| License | GPL-3.0-only |
| Author | Florian Eggenhofer |
| Maintainer | egg@informatik.uni-freiburg.de |
| Category | Bioinformatics |
| Source repo | head: git clone https://github.com/eggzilla/ClustalParser this: git clone https://github.com/eggzilla/ClustalParser/tree/1.3.0(tag 1.3.0) |
| Uploaded | by FlorianEggenhofer at 2019-11-14T21:55:39Z |
| Distributions | LTSHaskell:1.3.0, Stackage:1.3.0 |
| Reverse Dependencies | 3 direct, 0 indirect [details] |
| Executables | ClustalParserTest |
| Downloads | 11510 total (59 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
| Your Rating | |
| Status | Docs available [build log] Last success reported on 2019-11-14 [all 1 reports] |
Readme for ClustalParser-1.3.0
[back to package description]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 http://www.clustal.org/.
Mlocarna is a multiple sequence alignment tool for RNA sequences with secondary structure output. For more information on mlocarna refer to http://www.bioinf.uni-freiburg.de/Software/LocARNA/.
cmalign is a multiple sequence alignment program based on RNA family models and produces ,among others, clustal output. It is part of infernal http://infernal.janelia.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)