Package Bio :: Package Phylo :: Package Applications :: Module _Raxml :: Class RaxmlCommandline
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Class RaxmlCommandline

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                     object --+    
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Application.AbstractCommandline --+
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                                 RaxmlCommandline

Command-line wrapper for the tree inference program RAxML.

The required parameters are 'sequences' (-s), 'model' (-m) and 'name' (-n). The parameter 'parsimony_seed' (-p) must also be set for RAxML, but if you do not specify it, this wrapper will set the seed to 10000 for you.

Example:

>>> from Bio.Phylo.Applications import RaxmlCommandline
>>> raxml_cline = RaxmlCommandline(sequences="Tests/Phylip/interlaced2.phy",
...                                model="PROTCATWAG", name="interlaced2")
>>> print(raxml_cline)
raxmlHPC -m PROTCATWAG -n interlaced2 -p 10000 -s Tests/Phylip/interlaced2.phy

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

Citation:

Stamatakis A. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models. Bioinformatics 2006, 22(21):2688-2690.

Homepage: http://sco.h-its.org/exelixis/software.html

Instance Methods [hide private]
 
__init__(self, cmd='raxmlHPC', **kwargs)
Create a new instance of a command line wrapper object.
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Inherited from Application.AbstractCommandline: __call__, __repr__, __setattr__, __str__, set_parameter

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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='raxmlHPC', **kwargs)
(Constructor)

source code 
Create a new instance of a command line wrapper object.

Overrides: object.__init__
(inherited documentation)