Exercise 4 help file: A portion of output for 3 models: M0, M3, and M8.
The output is
annotated with information that will help you to complete exercise 4. Note that the
example output is for a different dataset than the one you will use in exercise 4.
Annotated portion of the results for codon model M0:
.
.
.
TREE # 1: ((((3, 4), 1), 2), 5);
MP score: 154
This is a rooted tree. Please check!
This is the log likelihood
lnL(ntime: 8 np: 10): -1055.334638
+0.000000
score
for
a
6..7
7..8
8..9
9..3
9..4
8..1(lnL) computed
7..2
6..5
dataset of0.231447
5 sequences.
0.600255 0.085489 0.209403 0.355149 0.794944 0.249128
0.575094 1.801114 0.079244
Note: Branch length is defined as number of nucleotide substitutions per codon (not per nucleotide
site).
tree length =
3.10091
((((3: 0.355149, 4: 0.794944): 0.209403, 1: 0.249128): 0.085489, 2: 0.231447): 0.600255, 5: 0.575094);
((((rabbit: 0.355149, rat: 0.794944): 0.209403, human: 0.249128): 0.085489, goat-cow: 0.231447):
0.600255, marsupial: 0.575094);
Detailed output identifying parameters
This is the ML estimate of
kappa under model M0.
kappa (ts/tv) = 1.80111
omega (dN/dS) =
.
.
.
0.07924
This is the ML estimate of
omega under model M0
Annotated portion of the results for codon model M3 with k=3 site classes:
.
.
.
Model 3: discrete (3 categories)
This is the log likelihood
TREE # 1: ((((3, 4), 1), 2), 5);
MP score:score
154 (lnL) computed for the
This is a rooted tree. Please check!
same dataset under M3
lnL(ntime: 8 np: 14): -1045.839986
+0.000000
6..7
7..8
8..9
9..3
9..4
8..1
7..2
6..5
0.695909 0.078848 0.194592 0.373577 0.883911 0.285355 0.219268 0.631211 1.823190 0.464043 0.514623
0.008677 0.142536 1.344918
Note: Branch length is defined as number of nucleotide substitutions per codon (not per nucleotide
site).
tree length =
3.36267
((((3: 0.373577, 4: 0.883911): 0.194592, 1: 0.285355): 0.078848, 2: 0.219268): 0.695909, 5: 0.631211);
((((rabbit: 0.373577, rat: 0.883911): 0.194592, human: 0.285355): 0.078848, goat-cow: 0.219268):
0.695909, marsupial: 0.631211);
Detailed output identifying parameters
kappa (ts/tv)
=
p0
p1.82319
p2
1
dN/dS for site classes (K=3)
p:
w:
.
.
.
0.46404
0.00868
0.51462
0.14254
0.02133
1.34492
ML estimates of proportions
for site classes 1, 2 & 3
ML estimates of omega
for site classes 1, 2 & 3
Annotated portion of the results for codon model M8:
.
.
.
Model 8: beta&w>1 (11 categories)
This is the log likelihood
TREE # 1: ((((3, 4), 1), 2), 5);
MP score:score
154 (lnL) computed for the
This is a rooted tree. Please check!
same dataset under M8
lnL(ntime: 8 np: 13): -1046.003808
+0.000000
6..7
7..8
8..9
9..3
9..4
8..1
7..2
6..5
0.694589 0.081476 0.198355 0.369476 0.877899 0.279892 0.219450 0.635145 1.831201 0.984555 0.693123
7.401686 1.438893
Note: Branch length is defined as number of nucleotide substitutions per codon (not per nucleotide
site).
tree length =
3.35628
((((3: 0.369476, 4: 0.877899): 0.198355, 1: 0.279892): 0.081476, 2: 0.219450): 0.694589, 5: 0.635145);
((((rabbit: 0.369476, rat: 0.877899): 0.198355, human: 0.279892): 0.081476, goat-cow: 0.219450):
0.694589, marsupial: 0.635145);
p0
Beta parameter
p
Detailed output
identifying
parameters
kappa (ts/tv) =
Parameters in M8 (beta&w>1):
p0= 0.98456 p= 0.69312 q=
(p1= 0.01544) w= 1.43889
.
.
.
NOTES:
1.83120
7.40169
Beta parameter
p and q are shape
parameters for the Beta
distribution
p0 is the proportion of
beta-distributed sites
p1
>1
p1 is the proportion of
sites having > 1
an is constrained > 1