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 | 0.40 |
| b | root | 0.30 |
| c | edge.0 | 0.15 |
| d | edge.0 | 0.20 |
| edge.0 | root | 0.10 |
| 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 | GGTTCTGTAAGGGCCTCTTGCTGGTTCGCGTGTGCGTCGGGGTGGGGTGCGGTGTACGAA |
| b | CC.GT..GT..CT.T......G..A.T.TTG..AAC.TTT.C....TCAT...TG..T.T |
| c | C..G....CT.CC....C.CTGT.A...TTG..A.T.G..CC....T.A..T.TG.A..T |
| d | CT..T...CT.CT...GC.T.AT.AC..TTG..A.C.G...CG..TTCA..T..G.G..C |
4 x 1000 (truncated to 4 x 60) dna alignment