Simulate an alignment¶
Section author: 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.
>>> import sys
>>> from cogent3 import make_tree
>>> from cogent3.evolve import substitution_model
Specify the 4 taxon tree,
>>> t = make_tree('(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);')
Define our Felsenstein 1981 substitution model.
>>> sm = substitution_model.TimeReversibleNucleotide(motif_probs = {'A': 0.5, 'C': 0.2,
... 'G': 0.2, 'T': 0.1}, model_gaps=False)
>>> lf = sm.make_likelihood_function(t)
>>> lf.set_constant_lengths()
>>> lf.set_name('F81 model')
>>> print(lf)
F81 model
number of free parameters = 0
==========================
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
--------------------------
====================================
A C G T
------------------------------------
0.5000 0.2000 0.2000 0.1000
------------------------------------
We’ll now create a simulated alignment of length 1000 nucleotides.
>>> simulated = lf.simulate_alignment(sequence_length=1000)
The result is a normal Cogent
alignment object, which can be used in the same way as any other alignment object.