--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Mar 18 03:59:30 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=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/HIV1_A1/ENV_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -48140.15 -48190.84
2 -48143.73 -48181.76
--------------------------------------
TOTAL -48140.82 -48190.14
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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/ADOPS/HIV1_A1/ENV_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} 7.924580 0.038989 7.531423 8.295759 7.921610 997.89 1115.63 1.000
r(A<->C){all} 0.137237 0.000026 0.127058 0.146250 0.137221 494.31 571.21 1.003
r(A<->G){all} 0.291069 0.000096 0.272852 0.310744 0.290791 208.45 262.94 1.008
r(A<->T){all} 0.058761 0.000009 0.052875 0.064499 0.058707 487.19 582.07 1.000
r(C<->G){all} 0.075342 0.000023 0.066137 0.084448 0.075257 465.61 488.87 1.000
r(C<->T){all} 0.346549 0.000111 0.325588 0.365750 0.346818 205.62 250.05 1.014
r(G<->T){all} 0.091042 0.000019 0.082465 0.099355 0.091067 640.52 641.94 1.000
pi(A){all} 0.389313 0.000041 0.377038 0.402714 0.389421 186.84 288.88 1.007
pi(C){all} 0.175724 0.000022 0.166923 0.185081 0.175724 295.69 404.61 1.002
pi(G){all} 0.216852 0.000026 0.206623 0.226496 0.216820 364.09 377.65 1.002
pi(T){all} 0.218110 0.000031 0.207745 0.229529 0.218010 462.31 482.06 1.009
alpha{1,2} 0.447391 0.000379 0.408282 0.483509 0.446617 1170.88 1257.11 1.000
alpha{3} 1.030798 0.004949 0.902775 1.171946 1.028718 1217.04 1259.96 1.000
pinvar{all} 0.143854 0.000182 0.116537 0.168512 0.144010 949.51 1031.44 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 -39389.370011
Model 2: PositiveSelection -38756.699399
Model 0: one-ratio -41701.418989
Model 3: discrete -38738.678452
Model 7: beta -39270.501835
Model 8: beta&w>1 -38676.877865
Model 0 vs 1 4624.097955999998
Model 2 vs 1 1265.3412240000034
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.GB.08.D650_E9.HQ595775_)
Pr(w>1) post mean +- SE for w
7 R 1.000** 3.625
10 H 0.993** 3.609
14 T 0.525 2.377
77 E 1.000** 3.626
126 N 1.000** 3.626
127 S 1.000** 3.626
128 S 1.000** 3.626
129 E 1.000** 3.626
130 E 1.000** 3.626
131 R 1.000** 3.626
132 G 1.000** 3.626
149 Q 0.999** 3.624
152 Y 0.911 3.393
164 D 1.000** 3.626
165 N 1.000** 3.626
166 T 1.000** 3.625
167 T 1.000** 3.626
177 V 0.822 3.160
184 S 0.999** 3.625
215 T 0.973* 3.554
252 L 0.987* 3.593
254 D 0.834 3.189
256 T 0.945 3.481
268 E 1.000** 3.626
275 N 1.000** 3.626
283 H 1.000** 3.626
294 E 1.000** 3.626
302 E 1.000** 3.626
305 Y 1.000** 3.626
306 Q 1.000** 3.626
308 V 1.000** 3.626
309 E 1.000** 3.626
314 Q 0.996** 3.616
319 V 1.000** 3.626
321 D 1.000** 3.626
322 Q 0.997** 3.618
323 S 1.000** 3.626
348 Q 1.000** 3.626
378 S 1.000** 3.626
380 P 1.000** 3.626
384 T 1.000** 3.626
398 N 1.000** 3.626
399 N 1.000** 3.626
400 D 1.000** 3.626
401 T 1.000** 3.626
436 R 1.000** 3.626
542 A 0.998** 3.620
547 N 1.000** 3.626
554 L 1.000** 3.626
555 E 1.000** 3.626
556 Y 1.000** 3.626
564 Q 0.984* 3.584
570 D 0.980* 3.573
574 N 1.000** 3.626
575 L 0.984* 3.583
578 T 1.000** 3.626
608 D 0.998** 3.620
654 H 0.514 2.349
655 H 1.000** 3.626
657 A 0.976* 3.564
658 P 0.700 2.839
680 G 0.999** 3.625
720 A 0.998** 3.620
760 I 0.995** 3.614
761 V 0.989* 3.596
764 T 1.000** 3.626
765 Y 1.000** 3.626
769 L 0.998** 3.621
779 L 0.840 3.206
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: B.GB.08.D650_E9.HQ595775_)
Pr(w>1) post mean +- SE for w
7 R 1.000** 3.499 +- 0.054
10 H 0.994** 3.484 +- 0.198
14 T 0.564 2.409 +- 1.240
77 E 1.000** 3.500 +- 0.000
125 D 0.507 2.268 +- 1.250
126 N 1.000** 3.500 +- 0.000
127 S 1.000** 3.500 +- 0.000
128 S 1.000** 3.500 +- 0.000
129 E 1.000** 3.500 +- 0.000
130 E 1.000** 3.500 +- 0.000
131 R 1.000** 3.500 +- 0.000
132 G 1.000** 3.500 +- 0.000
149 Q 0.999** 3.498 +- 0.062
152 Y 0.920 3.301 +- 0.677
164 D 1.000** 3.500 +- 0.000
165 N 1.000** 3.500 +- 0.000
166 T 1.000** 3.499 +- 0.037
167 T 1.000** 3.500 +- 0.000
177 V 0.836 3.089 +- 0.926
184 S 0.999** 3.498 +- 0.062
215 T 0.976* 3.441 +- 0.379
252 L 0.987* 3.466 +- 0.288
254 D 0.859 3.148 +- 0.870
256 T 0.949 3.373 +- 0.549
268 E 1.000** 3.500 +- 0.002
275 N 1.000** 3.500 +- 0.011
283 H 1.000** 3.500 +- 0.018
294 E 1.000** 3.500 +- 0.002
302 E 1.000** 3.500 +- 0.025
305 Y 1.000** 3.500 +- 0.030
306 Q 1.000** 3.500 +- 0.000
308 V 1.000** 3.500 +- 0.001
309 E 1.000** 3.500 +- 0.002
314 Q 0.996** 3.490 +- 0.156
319 V 1.000** 3.500 +- 0.001
321 D 1.000** 3.500 +- 0.003
322 Q 0.997** 3.493 +- 0.132
323 S 1.000** 3.500 +- 0.003
348 Q 1.000** 3.500 +- 0.000
378 S 1.000** 3.500 +- 0.002
380 P 1.000** 3.500 +- 0.001
384 T 1.000** 3.500 +- 0.003
398 N 1.000** 3.500 +- 0.000
399 N 1.000** 3.500 +- 0.000
400 D 1.000** 3.500 +- 0.000
401 T 1.000** 3.500 +- 0.002
436 R 1.000** 3.500 +- 0.024
542 A 0.998** 3.495 +- 0.117
547 N 1.000** 3.500 +- 0.001
554 L 1.000** 3.500 +- 0.000
555 E 1.000** 3.500 +- 0.000
556 Y 1.000** 3.500 +- 0.002
564 Q 0.985* 3.462 +- 0.308
570 D 0.983* 3.457 +- 0.325
574 N 1.000** 3.500 +- 0.000
575 L 0.985* 3.462 +- 0.305
578 T 1.000** 3.500 +- 0.000
608 D 0.998** 3.495 +- 0.117
654 H 0.547 2.366 +- 1.245
655 H 1.000** 3.500 +- 0.004
657 A 0.978* 3.445 +- 0.365
658 P 0.712 2.779 +- 1.132
680 G 0.999** 3.499 +- 0.058
684 N 0.549 2.371 +- 1.244
720 A 0.998** 3.494 +- 0.124
760 I 0.996** 3.490 +- 0.161
761 V 0.990* 3.475 +- 0.250
764 T 1.000** 3.500 +- 0.013
765 Y 1.000** 3.500 +- 0.001
769 L 0.998** 3.495 +- 0.115
779 L 0.853 3.133 +- 0.885
Model 8 vs 7 1187.247940000001
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.GB.08.D650_E9.HQ595775_)
Pr(w>1) post mean +- SE for w
7 R 1.000** 3.155
10 H 0.995** 3.145
14 T 0.667 2.414
77 E 1.000** 3.156
125 D 0.528 2.109
126 N 1.000** 3.156
127 S 1.000** 3.156
128 S 1.000** 3.156
129 E 1.000** 3.156
130 E 1.000** 3.156
131 R 1.000** 3.156
132 G 1.000** 3.156
149 Q 1.000** 3.155
152 Y 0.942 3.026
164 D 1.000** 3.156
165 N 1.000** 3.156
166 T 1.000** 3.156
167 T 1.000** 3.156
177 V 0.894 2.921
184 S 1.000** 3.155
215 T 0.977* 3.105
252 L 0.990** 3.134
254 D 0.877 2.884
256 T 0.966* 3.081
268 E 1.000** 3.156
275 N 1.000** 3.156
283 H 1.000** 3.156
294 E 1.000** 3.156
302 E 1.000** 3.156
305 Y 1.000** 3.156
306 Q 1.000** 3.156
308 V 1.000** 3.156
309 E 1.000** 3.156
314 Q 0.997** 3.149
319 V 1.000** 3.156
321 D 1.000** 3.156
322 Q 0.998** 3.151
323 S 1.000** 3.156
348 Q 1.000** 3.156
378 S 1.000** 3.156
380 P 1.000** 3.156
384 T 1.000** 3.156
398 N 1.000** 3.156
399 N 1.000** 3.156
400 D 1.000** 3.156
401 T 1.000** 3.156
436 R 1.000** 3.156
542 A 0.998** 3.152
547 N 1.000** 3.156
554 L 1.000** 3.156
555 E 1.000** 3.156
556 Y 1.000** 3.156
564 Q 0.988* 3.130
570 D 0.985* 3.122
574 N 1.000** 3.156
575 L 0.988* 3.129
578 T 1.000** 3.156
608 D 0.998** 3.152
654 H 0.656 2.385
655 H 1.000** 3.156
657 A 0.983* 3.119
658 P 0.791 2.688
680 G 0.999** 3.155
684 N 0.613 2.295
720 A 0.998** 3.153
760 I 0.996** 3.148
761 V 0.991** 3.136
764 T 1.000** 3.156
765 Y 1.000** 3.156
769 L 0.999** 3.153
779 L 0.885 2.900
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: B.GB.08.D650_E9.HQ595775_)
Pr(w>1) post mean +- SE for w
7 R 0.999** 3.498 +- 0.079
10 H 0.981* 3.451 +- 0.352
77 E 1.000** 3.500 +- 0.000
126 N 1.000** 3.500 +- 0.001
127 S 1.000** 3.500 +- 0.000
128 S 1.000** 3.500 +- 0.000
129 E 1.000** 3.500 +- 0.000
130 E 1.000** 3.500 +- 0.000
131 R 1.000** 3.500 +- 0.000
132 G 1.000** 3.500 +- 0.000
149 Q 0.999** 3.497 +- 0.087
152 Y 0.772 2.913 +- 1.080
164 D 1.000** 3.500 +- 0.001
165 N 1.000** 3.500 +- 0.000
166 T 0.999** 3.498 +- 0.074
167 T 1.000** 3.500 +- 0.000
177 V 0.664 2.634 +- 1.219
184 S 0.999** 3.498 +- 0.078
215 T 0.889 3.215 +- 0.806
252 L 0.974* 3.433 +- 0.411
254 D 0.544 2.326 +- 1.281
256 T 0.870 3.166 +- 0.865
268 E 1.000** 3.500 +- 0.004
275 N 1.000** 3.500 +- 0.017
283 H 1.000** 3.500 +- 0.032
294 E 1.000** 3.500 +- 0.003
302 E 1.000** 3.499 +- 0.049
305 Y 0.999** 3.499 +- 0.059
306 Q 1.000** 3.500 +- 0.000
308 V 1.000** 3.500 +- 0.001
309 E 1.000** 3.500 +- 0.003
314 Q 0.989* 3.472 +- 0.269
319 V 1.000** 3.500 +- 0.001
321 D 1.000** 3.500 +- 0.005
322 Q 0.991** 3.477 +- 0.244
323 S 1.000** 3.500 +- 0.003
348 Q 1.000** 3.500 +- 0.000
378 S 1.000** 3.500 +- 0.004
380 P 1.000** 3.500 +- 0.001
384 T 1.000** 3.500 +- 0.004
398 N 1.000** 3.500 +- 0.000
399 N 1.000** 3.500 +- 0.001
400 D 1.000** 3.500 +- 0.000
401 T 1.000** 3.500 +- 0.004
436 R 1.000** 3.499 +- 0.038
542 A 0.993** 3.483 +- 0.208
547 N 1.000** 3.500 +- 0.001
554 L 1.000** 3.500 +- 0.000
555 E 1.000** 3.500 +- 0.000
556 Y 1.000** 3.500 +- 0.003
564 Q 0.958* 3.391 +- 0.518
570 D 0.920 3.295 +- 0.695
574 N 1.000** 3.500 +- 0.000
575 L 0.951* 3.375 +- 0.553
578 T 1.000** 3.500 +- 0.000
608 D 0.991** 3.477 +- 0.241
655 H 1.000** 3.500 +- 0.005
657 A 0.932 3.326 +- 0.646
680 G 0.998** 3.496 +- 0.107
720 A 0.995** 3.488 +- 0.175
760 I 0.984* 3.459 +- 0.321
761 V 0.960* 3.398 +- 0.502
764 T 1.000** 3.500 +- 0.021
765 Y 1.000** 3.500 +- 0.001
769 L 0.997** 3.491 +- 0.149
779 L 0.630 2.546 +- 1.246
