Simulate an alignment#
Section author: Gavin Huttley
Note
These docs now use the new_type core objects via the following setting.
import os
# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"
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 | TCTAGGGCGGTGGGTGCTCCTGTCAGGTTTCCGTCATTTCGGGTCTTCTCCCTGTCTAGT |
| b | CG.C..CGT.GT.CG.T.T.AT.G.T.G..G...A.G.G...T......G.G..CAG.T. |
| c | ...CA.TG.CGTT.G.G.T..C.T.C.GC...T...A.GT.C...CCA.G....ATAT.. |
| d | .GCT..TA.CGTT.G.G.T.CC.G...G.G..T...A.GT......CAGT....ATG... |
4 x 1000 (truncated to 4 x 60) dna alignment