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
aroot0.40
broot0.30
cedge.00.15
dedge.00.20
edge.0root0.10
Motif params
ACGT
0.100.200.300.40

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

simulated = lf.simulate_alignment(sequence_length=1000)
simulated
0
aTCTTCCTCGTTTAGTGTCGTGGTAAATTGGATTTTCGGTGTGGGGTGTTGAGTTGTCACC
b.GAG.T..CG...T.TAG.ATC.TTTG....GC.A.....C.CT.G..AC..CC.CGG.G
c.GGG.TA..GC.T..TC....C.TTTGA.A.C........CTCT....AC....TCGTGG
d.TGG.TA..G..T.GTCA..TCGTTT.G.C.C........C.CT....ACT...TCGG.T

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