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object --+ | Application.AbstractCommandline --+ | MuscleCommandline
Command line wrapper for the multiple alignment program MUSCLE.
http://www.drive5.com/muscle/
Example:
>>> from Bio.Align.Applications import MuscleCommandline >>> muscle_exe = r"C:\Program Files\Aligments\muscle3.8.31_i86win32.exe" >>> in_file = r"C:\My Documents\unaligned.fasta" >>> out_file = r"C:\My Documents\aligned.fasta" >>> muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file) >>> print muscle_cline C:\Program Files\Aligments\muscle3.8.31_i86win32.exe -in "C:\My Documents\unaligned.fasta" -out "C:\My Documents\aligned.fasta"
You would typically run the command line with muscle_cline() or via the Python subprocess module, as described in the Biopython tutorial.
Citations:
Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113.
Last checked against version: 3.7, briefly against 3.8
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Create a new instance of a command line wrapper object.
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