Class TCoffeeCommandline

source code

                     object --+    
                              |    
Application.AbstractCommandline --+
                                  |
                                 TCoffeeCommandline

Commandline object for the TCoffee alignment program.

http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

The T-Coffee command line tool has a lot of switches and options. This wrapper implements a VERY limited number of options - if you would like to help improve it please get in touch.

Example:

To align a FASTA file (unaligned.fasta) with the output in ClustalW format (file aligned.aln), and otherwise default settings, use:

>>> from Bio.Align.Applications import TCoffeeCommandline
>>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta",
...                                    output="clustalw",
...                                    outfile="aligned.aln")
>>> print tcoffee_cline
t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln

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

Citation:

T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins, Heringa, JMB,302(205-217) 2000

Last checked against: Version_6.92