natsel_neutral – a test for selective neutrality

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"

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

LR	df	pvalue
4.5034	1	0.0338

hypothesis	key	lnL	nfp	DLC	unique_Q
null	'GNC-null'	-6715.5260	22	True	True
alt	'GNC-alt'	-6713.2743	23	True	True

result.alt.lf

GNC-alt

log-likelihood = -6713.2743

number of free parameters = 23

Global params

A>C	A>G	A>T	C>A	C>G	C>T	G>A	G>C	G>T	T>A
0.8614	3.5373	0.9792	1.6667	2.2042	6.2565	7.9195	1.2253	0.8014	1.2911

continuation

T>C	omega
3.0723	0.8204

Edge params

edge	parent	length
Galago	root	0.5232
HowlerMon	root	0.1338
Rhesus	edge.3	0.0640
Orangutan	edge.2	0.0233
Gorilla	edge.1	0.0075
Human	edge.0	0.0182
Chimpanzee	edge.0	0.0085
edge.0	edge.1	0.0000
edge.1	edge.2	0.0100
edge.2	edge.3	0.0366
edge.3	root	0.0238

Motif params

AAA	AAC	AAG	AAT	ACA	ACC	ACG	ACT	AGA	AGC
0.0556	0.0235	0.0344	0.0556	0.0228	0.0046	0.0008	0.0289	0.0231	0.0286

continuation

AGG	AGT	ATA	ATC	ATG	ATT	CAA	CAC	CAG	CAT
0.0140	0.0381	0.0186	0.0070	0.0128	0.0192	0.0196	0.0052	0.0238	0.0221

continuation

CCA	CCC	CCG	CCT	CGA	CGC	CGG	CGT	CTA	CTC
0.0195	0.0062	0.0006	0.0263	0.0011	0.0009	0.0023	0.0032	0.0137	0.0078

continuation

CTG	CTT	GAA	GAC	GAG	GAT	GCA	GCC	GCG	GCT
0.0125	0.0105	0.0755	0.0105	0.0303	0.0315	0.0158	0.0096	0.0014	0.0137

continuation

GGA	GGC	GGG	GGT	GTA	GTC	GTG	GTT	TAC	TAT
0.0161	0.0090	0.0067	0.0133	0.0148	0.0070	0.0069	0.0213	0.0023	0.0101

continuation

TCA	TCC	TCG	TCT	TGC	TGG	TGT	TTA	TTC	TTG
0.0221	0.0082	0.0015	0.0251	0.0018	0.0040	0.0201	0.0212	0.0078	0.0108

continuation

TTT
0.0187