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. (Note I’m setting optimise_motif_probs=False
to speed up execution of the examples, not because it’s a good idea!)
cogent3.app.result.hypothesis_result
Statistics
LR |
df |
pvalue |
4.5034 |
1 |
0.0338 |
hypothesis |
key |
lnL |
nfp |
DLC |
unique_Q |
null |
'GNC-null' |
-6715.5250 |
22 |
True |
|
alt |
'GNC-alt' |
-6713.2733 |
23 |
True |
|
GNC-alt
log-likelihood = -6713.2733
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 |
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 |
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 |
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 |
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 |
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 |
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 |