Simulate an alignment¶
Section author: Gavin Huttley
For this example we just create a simple model using a four taxon tree with different branch lengths and a Felsenstein model.
import sys
from cogent3 import make_tree
from cogent3.evolve.models import get_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 = 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
F81
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 |
---|---|---|---|
0.1000 | 0.2000 | 0.3000 | 0.4000 |
We’ll now create a simulated alignment of length 1000 nucleotides.
simulated = lf.simulate_alignment(sequence_length=1000)
simulated
0 | |
a | GTGGGTTTCTTCTTTGGGCTCGGCGGGTGGTTCTGTTGGTGGTTCCGTATCTAGCGGTCA |
b | ...T...C.C.TA.CC......TG.C..C..AT....AA.TCCCT.T.....GT....G. |
c | .A.A...C.G.T.ACT.......TC......CT..GGTT.TCCGG.T.....TCA..C.. |
d | ...AT..C.G.T...CTT.....T......G.T.TGGT..T.CCG.C.T...GC...CA. |
4 x 1000 (truncated to 4 x 60) dna alignment