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# Class MuscleCommandline

source code

```                     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

 Instance Methods

 __init__(self, cmd=`'``muscle``'`, **kwargs) Create a new instance of a command line wrapper object. source code

Inherited from `Application.AbstractCommandline`: `__call__`, `__repr__`, `__setattr__`, `__str__`, `set_parameter`

Inherited from `Application.AbstractCommandline` (private): `_check_value`, `_clear_parameter`, `_get_parameter`, `_validate`

Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__sizeof__`, `__subclasshook__`

 Properties

Inherited from `object`: `__class__`

 Method Details

### __init__(self, cmd=`'``muscle``'`, **kwargs)(Constructor)

source code
Create a new instance of a command line wrapper object.
Overrides: object.__init__
(inherited documentation)

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