natsel_timehet
– a test of branch heterogeneity
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). (Note I’m setting optimise_motif_probs=False
to speed up execution of the examples, not because it’s a good idea!)
Statistics
LR |
df |
pvalue |
4.9248 |
1 |
0.0265 |
hypothesis |
key |
lnL |
nfp |
DLC |
unique_Q |
null |
'GNC-null' |
-6713.2733 |
23 |
True |
|
alt |
'GNC-alt' |
-6710.8109 |
24 |
True |
|
GNC-alt
log-likelihood = -6710.8109
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 |
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 |
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 |