ClustalParser
Libary for parsing Clustal tools output
| Version on this page: | 1.2.1 |
| LTS Haskell 23.1: | 1.3.0 |
| Stackage Nightly 2024-12-22: | 1.3.0 |
| Latest on Hackage: | 1.3.0 |
Maintained by [email protected]
This version can be pinned in stack with:
ClustalParser-1.2.1@sha256:82a423ae68d4adb4b28e2b3c79a8b4f3479a51045139c36b3dd512fb8a503041,2692Module documentation for 1.2.1
Depends on 7 packages(full list with versions):
Used by 1 package in nightly-2018-01-25(full list with versions):
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)