ClustalParser

Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna

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 molocarna 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)