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)