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README
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)