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Simulate an alignment
=====================
.. sectionauthor:: Gavin Huttley
How to simulate an alignment. For this example we just create a simple model using a four taxon tree with very different branch lengths, a Felsenstein model with very different nucleotide frequencies and a long alignment.
See the other examples for how to define other substitution models.
.. doctest::
>>> import sys
>>> from cogent import LoadTree
>>> from cogent.evolve import substitution_model
Specify the 4 taxon tree,
.. doctest::
>>> t = LoadTree(treestring='(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);')
Define our Felsenstein 1981 substitution model.
.. doctest::
>>> sm = substitution_model.Nucleotide(motif_probs = {'A': 0.5, 'C': 0.2,
... 'G': 0.2, 'T': 0.1}, model_gaps=False)
>>> lf = sm.makeLikelihoodFunction(t)
>>> lf.setConstantLengths()
>>> lf.setName('F81 model')
>>> print lf
F81 model
==========================
edge parent length
--------------------------
a root 0.4000
b root 0.3000
c edge.0 0.1500
d edge.0 0.2000
edge.0 root 0.1000
--------------------------
===============
motif mprobs
---------------
T 0.1000
C 0.2000
A 0.5000
G 0.2000
---------------
We'll now create a simulated alignment of length 1000 nucleotides.
.. doctest::
>>> simulated = lf.simulateAlignment(sequence_length=1000)
The result is a normal ``Cogent`` alignment object, which can be used in the same way as any other alignment object.
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