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 | 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 | CGCGGAAGTCCGCTATTTGTGGTTACGAGTTGGTTATGGGGGCACTGGGCCGGTTATCTA |
| 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