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/.
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)
* Fixed compiler warnings and updated documentation to mention structural clustal format
* Added -Wall and -O2 compiler options
* Added support for clustal alignments with secondary structure annotation