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 params
edgeparentlength
aroot0.4000
broot0.3000
cedge.00.1500
dedge.00.2000
edge.0root0.1000
Motif params
ACGT
0.10000.20000.30000.4000

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

simulated = lf.simulate_alignment(sequence_length=1000)
simulated
0
aCGCGGAAGTCCGCTATTTGTGGTTACGAGTTGGTTATGGGGGCACTGGGCCGGTTATCTA
b..TT..TC.T....GGG....C.CGT.C..CC....G..TTCT.G...A...CC..C...
c....T.T.A.......G..G.C.GGT.C.CCT.C..G..C..T...T..G..CC..C..C
d..T.T.T.G...TGT.G..G.C..GT.C..CC.C..G..C..TC.....T..CC..CTC.

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