`natsel_timehet` – a test of branch heterogeneity#

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 whether the mode of natural selection affecting human and chimpanzee lineages is distinctive. This is done by specifying the edges of interest (Yang 1998).

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")

hc_differ = get_app("natsel_timehet",
    "GNC",
    tree="data/primate_brca1.tree",
    optimise_motif_probs=False,
    tip1="Human",
    tip2="Chimpanzee",
)
result = hc_differ(aln)
result

Statistics
LR	df	pvalue
4.9248	1	0.0265

hypothesis	key	lnL	nfp	DLC	unique_Q
null	'GNC-null'	-6713.2743	23	True	True
alt	'GNC-alt'	-6710.8118	24	True	True

result.alt.lf

GNC-alt

log-likelihood = -6710.8118

number of free parameters = 24

Global params
A>C	A>G	A>T	C>A	C>G	C>T	G>A	G>C	G>T	T>A
0.8620	3.5361	0.9790	1.6698	2.2059	6.2630	7.9209	1.2265	0.8024	1.2882

continuation
T>C
3.0675

Edge params
edge	parent	length	omega
Galago	root	0.5237	0.7906
HowlerMon	root	0.1339	0.7906
Rhesus	edge.3	0.0640	0.7906
Orangutan	edge.2	0.0233	0.7906
Gorilla	edge.1	0.0075	0.7906
Human	edge.0	0.0182	2.6351
Chimpanzee	edge.0	0.0085	2.6351
edge.0	edge.1	0.0000	0.7906
edge.1	edge.2	0.0100	0.7906
edge.2	edge.3	0.0366	0.7906
edge.3	root	0.0238	0.7906

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

natsel_timehet – a test of branch heterogeneity#

GNC-alt

`natsel_timehet` – a test of branch heterogeneity#