natsel_neutral – a test for selective neutrality#

We employ codon models to test hypotheses regarding the mode of natural selection that has operated on a gene.

Noting that ω (omega) is the ratio of nonsynonymous substitutions to synonymous substitutions, ω=1 is indicative a gene is evolving neutrally.

Warning

I’m setting optimise_motif_probs=False to speed up execution of the examples, not because it’s a good idea!

from cogent3 import get_app

loader = get_app("load_aligned", format="fasta", moltype="dna")
aln = loader("data/primate_brca1.fasta")

omega_eq_1 = get_app("natsel_neutral",
    "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False
)
result = omega_eq_1(aln)
type(result)

cogent3.app.result.hypothesis_result

result
Statistics
LRdfpvalue
4.503410.0338
hypothesiskeylnLnfpDLCunique_Q
null'GNC-null'-6715.526022TrueTrue
alt'GNC-alt'-6713.274323TrueTrue
 
result.alt.lf

GNC-alt

log-likelihood = -6713.2743

number of free parameters = 23

Global params
A>CA>GA>TC>AC>GC>TG>AG>CG>TT>A
0.86143.53730.97921.66672.20426.25657.91951.22530.80141.2911
continuation
T>Comega
3.07230.8204
Edge params
edgeparentlength
Galagoroot0.5232
HowlerMonroot0.1338
Rhesusedge.30.0640
Orangutanedge.20.0233
Gorillaedge.10.0075
Humanedge.00.0182
Chimpanzeeedge.00.0085
edge.0edge.10.0000
edge.1edge.20.0100
edge.2edge.30.0366
edge.3root0.0238
Motif params
AAAAACAAGAATACAACCACGACTAGAAGC
0.05560.02350.03440.05560.02280.00460.00080.02890.02310.0286
continuation
AGGAGTATAATCATGATTCAACACCAGCAT
0.01400.03810.01860.00700.01280.01920.01960.00520.02380.0221
continuation
CCACCCCCGCCTCGACGCCGGCGTCTACTC
0.01950.00620.00060.02630.00110.00090.00230.00320.01370.0078
continuation
CTGCTTGAAGACGAGGATGCAGCCGCGGCT
0.01250.01050.07550.01050.03030.03150.01580.00960.00140.0137
continuation
GGAGGCGGGGGTGTAGTCGTGGTTTACTAT
0.01610.00900.00670.01330.01480.00700.00690.02130.00230.0101
continuation
TCATCCTCGTCTTGCTGGTGTTTATTCTTG
0.02210.00820.00150.02510.00180.00400.02010.02120.00780.0108
continuation
TTT
0.0187