Simulate an alignment

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 params

edge	parent	length
a	root	0.40
b	root	0.30
c	edge.0	0.15
d	edge.0	0.20
edge.0	root	0.10

Motif params

A	C	G	T
0.10	0.20	0.30	0.40

We’ll now create a simulated alignment of length 1000 nucleotides.

simulated = lf.simulate_alignment(sequence_length=1000)
simulated

	0
a	CGTCTTCCGGGTCCTCTGCGGTGTTTCCTTTTGTGTCAGGTCAAGATTCTGCGCAATAGT
b	....AGTA.C...TG....TC..CG.T.G..G...GT..........G..T.....C...
c	AT..CC.G.....TGG.T.CA..CGCT..C.G...GT.......CGGG........CCT.
d	A...C..G..T..T.G...C...CGCTT..GG.C.GT....GT.TGCG......G.CGT.

4 x 1000 (truncated to 4 x 60) dna alignment