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Simulate an alignment
=====================
.. sectionauthor:: Gavin Huttley
For this example we just create a simple model using a four taxon tree with different branch lengths and a Felsenstein model.
.. jupyter-execute::
import sys
from cogent3 import make_tree
from cogent3.evolve.models import get_model
Specify the 4 taxon tree,
.. jupyter-execute::
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.
.. jupyter-execute::
sm = get_model("F81")
lf = sm.make_likelihood_function(t)
lf.set_constant_lengths()
lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4))
lf
We'll now create a simulated alignment of length 1000 nucleotides.
.. jupyter-execute::
simulated = lf.simulate_alignment(sequence_length=1000)
simulated
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