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.