--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Mar 24 14:59:40 WET 2018
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS1/HIV1_AMINO/POL_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)
(Values are saved to the file /opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -31867.45 -31913.67
2 -31866.78 -31913.73
--------------------------------------
TOTAL -31867.06 -31913.70
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.418357 0.009402 3.230166 3.617533 3.418511 1310.89 1353.43 1.000
r(A<->C){all} 0.079808 0.000017 0.072261 0.088290 0.079717 534.29 599.90 1.000
r(A<->G){all} 0.363347 0.000167 0.338050 0.387642 0.362953 209.67 283.79 1.000
r(A<->T){all} 0.035486 0.000006 0.030684 0.040567 0.035441 908.84 942.87 1.000
r(C<->G){all} 0.036263 0.000017 0.027865 0.043847 0.036092 569.57 616.00 1.000
r(C<->T){all} 0.448445 0.000186 0.421849 0.474013 0.448931 198.90 291.07 1.001
r(G<->T){all} 0.036651 0.000012 0.030062 0.043475 0.036508 666.35 727.15 1.003
pi(A){all} 0.411384 0.000051 0.397827 0.425843 0.411284 530.99 734.49 1.000
pi(C){all} 0.178748 0.000031 0.168612 0.189812 0.178765 505.31 549.76 1.001
pi(G){all} 0.208938 0.000036 0.197626 0.221079 0.208697 591.99 595.90 1.000
pi(T){all} 0.200930 0.000035 0.189085 0.212477 0.200756 688.03 689.13 1.000
alpha{1,2} 0.283481 0.000253 0.252200 0.313110 0.282770 1024.07 1093.12 1.000
alpha{3} 2.212637 0.050530 1.830136 2.690248 2.189349 1202.43 1237.25 1.001
pinvar{all} 0.265349 0.000354 0.231083 0.305367 0.265586 1084.49 1108.16 1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.
Setting sumt conformat to Simple
--- CODEML SUMMARY
Model 1: NearlyNeutral -31214.748226
Model 2: PositiveSelection -31088.616652
Model 0: one-ratio -32862.797222
Model 3: discrete -30879.558554
Model 7: beta -30961.122093
Model 8: beta&w>1 -30816.421152
Model 0 vs 1 3296.0979920000027
Model 2 vs 1 252.26314799999818
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_)
Pr(w>1) post mean +- SE for w
17 P 0.997** 3.112
21 T 0.608 2.290
32 Q 0.939 2.990
34 R 0.960* 3.034
36 L 1.000** 3.120
39 Q 0.781 2.656
41 L 0.789 2.671
42 N 1.000** 3.120
43 F 0.578 2.225
62 I 0.935 2.981
106 P 1.000** 3.120
265 S 1.000** 3.120
304 S 1.000** 3.119
349 E 0.925 2.960
353 K 0.803 2.703
357 T 0.976* 3.070
387 Q 0.989* 3.096
428 T 0.982* 3.080
476 Q 1.000** 3.120
499 M 0.843 2.788
518 A 0.967* 3.049
519 L 1.000** 3.119
610 S 0.999** 3.118
625 Q 1.000** 3.119
633 S 0.999** 3.118
696 K 1.000** 3.120
821 S 0.995** 3.108
826 N 0.994** 3.107
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_)
Pr(w>1) post mean +- SE for w
17 P 0.998** 3.488 +- 0.145
21 T 0.559 2.393 +- 1.239
32 Q 0.951* 3.371 +- 0.544
34 R 0.964* 3.403 +- 0.472
36 L 1.000** 3.494 +- 0.080
39 Q 0.723 2.802 +- 1.118
41 L 0.756 2.883 +- 1.074
42 N 1.000** 3.494 +- 0.080
43 F 0.557 2.387 +- 1.240
62 I 0.912 3.275 +- 0.709
106 P 1.000** 3.494 +- 0.080
265 S 1.000** 3.494 +- 0.080
304 S 1.000** 3.493 +- 0.091
349 E 0.909 3.268 +- 0.720
353 K 0.798 2.989 +- 1.004
357 T 0.979* 3.441 +- 0.368
387 Q 0.990** 3.469 +- 0.260
428 T 0.984* 3.454 +- 0.321
476 Q 1.000** 3.494 +- 0.080
499 M 0.683 2.701 +- 1.162
518 A 0.969* 3.416 +- 0.440
519 L 1.000** 3.493 +- 0.085
610 S 1.000** 3.493 +- 0.091
625 Q 1.000** 3.493 +- 0.085
633 S 0.999** 3.492 +- 0.102
696 K 1.000** 3.494 +- 0.080
821 S 0.994** 3.480 +- 0.201
826 N 0.994** 3.477 +- 0.215
Model 8 vs 7 289.40188200000557
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_)
Pr(w>1) post mean +- SE for w
17 P 1.000** 2.587
21 T 0.900 2.403
32 Q 0.984* 2.559
34 R 0.994** 2.577
36 L 1.000** 2.588
39 Q 0.950 2.495
41 L 0.956* 2.507
42 N 1.000** 2.588
43 F 0.846 2.304
62 I 0.992** 2.573
106 P 1.000** 2.588
265 S 1.000** 2.588
304 S 1.000** 2.588
349 E 0.991** 2.571
353 K 0.975* 2.543
357 T 0.997** 2.582
387 Q 0.999** 2.586
428 T 0.998** 2.584
476 Q 1.000** 2.588
499 M 0.990** 2.570
518 A 0.996** 2.580
519 L 1.000** 2.588
610 S 1.000** 2.588
625 Q 1.000** 2.588
633 S 1.000** 2.588
696 K 1.000** 2.588
776 L 0.635 1.906
821 S 1.000** 2.587
826 N 1.000** 2.587
Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118)
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_)
Pr(w>1) post mean +- SE for w
17 P 0.999** 2.498 +- 0.054
21 T 0.896 2.332 +- 0.493
32 Q 0.980* 2.467 +- 0.227
34 R 0.989* 2.483 +- 0.163
36 L 1.000** 2.500 +- 0.001
39 Q 0.928 2.385 +- 0.412
41 L 0.944 2.410 +- 0.369
42 N 1.000** 2.500 +- 0.006
43 F 0.860 2.273 +- 0.564
62 I 0.981* 2.470 +- 0.214
106 P 1.000** 2.500 +- 0.001
265 S 1.000** 2.500 +- 0.007
304 S 1.000** 2.500 +- 0.020
349 E 0.976* 2.463 +- 0.240
353 K 0.953* 2.426 +- 0.334
357 T 0.994** 2.490 +- 0.124
387 Q 0.997** 2.495 +- 0.093
428 T 0.995** 2.492 +- 0.110
476 Q 1.000** 2.500 +- 0.003
499 M 0.971* 2.454 +- 0.266
518 A 0.992** 2.487 +- 0.142
519 L 1.000** 2.500 +- 0.012
610 S 1.000** 2.500 +- 0.026
625 Q 1.000** 2.500 +- 0.016
633 S 1.000** 2.499 +- 0.028
696 K 1.000** 2.500 +- 0.001
776 L 0.717 2.029 +- 0.753
821 S 0.998** 2.498 +- 0.063
826 N 0.998** 2.497 +- 0.064
