ClustalParser: Libary for parsing Clustal tools output
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Warnings:
- 'ghc-options: -O2' is rarely needed. Check that it is giving a real benefit and not just imposing longer compile times on your users.
- Exposed modules use unallocated top-level names: Bio
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.
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Properties
| Versions | 1.0.0, 1.0.1, 1.0.2, 1.0.3, 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 2015-04-21T09:00:17Z |
Modules
[Index]
Downloads
- ClustalParser-1.0.3.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
Package maintainers
For package maintainers and hackage trustees
Readme for ClustalParser-1.0.3
[back to package description]ClustalParser 
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)