Class ClustalOmegaCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 ClustalOmegaCommandline

Command line wrapper for clustal omega

http://www.clustal.org/omega

Example:

>>> from Bio.Align.Applications import ClustalOmegaCommandline
>>> in_file = "unaligned.fasta"
>>> out_file = "aligned.fasta"
>>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True)
>>> print clustalomega_cline
clustalo -i unaligned.fasta -o aligned.fasta --auto -v


You would typically run the command line with clustalomega_cline() or via
the Python subprocess module, as described in the Biopython tutorial.

Citation:

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R,
McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011).
Fast, scalable generation of high-quality protein multiple
sequence alignments using Clustal Omega.
Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75

Last checked against versions: 1.1.0

Create a new instance of a command line wrapper object.