Class ClustalwCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 ClustalwCommandline

Command line wrapper for clustalw (version one or two).

http://www.clustal.org/

Example:

>>> from Bio.Align.Applications import ClustalwCommandline
>>> in_file = "unaligned.fasta"
>>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)
>>> print clustalw_cline
clustalw2 -infile=unaligned.fasta

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

Citation:

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.

Last checked against versions: 1.83 and 2.0.10