--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Mar 15 21:22:40 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=/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_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -49253.20 -49295.51
2 -49251.92 -49291.59
--------------------------------------
TOTAL -49252.37 -49294.83
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 8.520280 0.070648 8.006031 9.029888 8.512646 880.50 906.37 1.000
r(A<->C){all} 0.132237 0.000027 0.121210 0.141730 0.132403 346.67 409.01 1.000
r(A<->G){all} 0.299126 0.000140 0.276629 0.321858 0.299409 172.85 225.56 1.001
r(A<->T){all} 0.056602 0.000011 0.050060 0.062777 0.056502 601.82 674.36 1.000
r(C<->G){all} 0.067927 0.000023 0.058703 0.077256 0.067770 517.03 613.55 1.003
r(C<->T){all} 0.346730 0.000156 0.323732 0.371366 0.346299 206.96 215.76 1.001
r(G<->T){all} 0.097379 0.000026 0.087467 0.106972 0.097266 366.65 396.22 1.004
pi(A){all} 0.397327 0.000049 0.383806 0.410914 0.397330 410.80 426.42 1.000
pi(C){all} 0.175425 0.000028 0.164550 0.184760 0.175509 266.64 299.75 1.000
pi(G){all} 0.220099 0.000034 0.208299 0.231055 0.219879 180.26 296.49 1.000
pi(T){all} 0.207149 0.000035 0.194870 0.218344 0.207041 361.43 385.63 1.000
alpha{1,2} 0.483374 0.000519 0.442819 0.528907 0.482658 1051.31 1087.49 1.000
alpha{3} 1.056696 0.004022 0.925692 1.174112 1.056890 985.27 1052.47 1.000
pinvar{all} 0.187538 0.000204 0.160950 0.216355 0.187694 1031.23 1058.84 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 -40805.901807
Model 2: PositiveSelection -40168.634087
Model 0: one-ratio -43375.868154
Model 3: discrete -40136.944168
Model 7: beta -40606.662897
Model 8: beta&w>1 -40033.544763
Model 0 vs 1 5139.932694000003
Model 2 vs 1 1274.535440000007
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.TH.06.98PB2.EU743784_)
Pr(w>1) post mean +- SE for w
10 W 1.000** 3.483
15 T 0.990** 3.459
73 Y 1.000** 3.483
119 P 1.000** 3.483
120 T 1.000** 3.482
121 T 1.000** 3.483
122 S 1.000** 3.483
139 K 0.871 3.162
140 Q 1.000** 3.483
143 Y 0.987* 3.451
155 N 0.995** 3.471
156 K 1.000** 3.483
157 T 1.000** 3.483
158 T 1.000** 3.483
168 V 0.998** 3.479
177 S 0.541 2.344
200 N 0.546 2.357
208 N 0.992** 3.462
249 T 0.956* 3.373
259 S 0.575 2.429
261 Q 1.000** 3.483
268 S 0.999** 3.480
276 H 1.000** 3.483
286 D 1.000** 3.483
299 G 0.992** 3.463
300 T 1.000** 3.483
303 E 0.998** 3.479
306 K 1.000** 3.483
307 Q 1.000** 3.483
309 A 1.000** 3.483
310 K 1.000** 3.483
313 K 1.000** 3.483
315 H 0.780 2.938
319 V 1.000** 3.483
323 S 0.999** 3.481
347 S 0.575 2.428
348 Q 1.000** 3.483
352 A 0.962* 3.388
354 T 1.000** 3.483
355 I 1.000** 3.483
357 S 1.000** 3.483
358 T 0.970* 3.408
385 S 1.000** 3.483
387 V 1.000** 3.483
391 L 1.000** 3.483
405 N 1.000** 3.483
406 T 1.000** 3.483
407 A 1.000** 3.483
456 I 0.779 2.934
548 A 1.000** 3.483
553 S 0.999** 3.481
560 Y 1.000** 3.483
561 D 1.000** 3.483
562 T 1.000** 3.483
570 K 0.556 2.379
576 S 0.691 2.717
580 D 1.000** 3.483
581 L 1.000** 3.483
584 G 1.000** 3.483
614 D 0.998** 3.479
661 T 1.000** 3.483
663 H 0.988* 3.453
664 Q 0.903 3.242
686 V 1.000** 3.483
690 S 0.999** 3.481
696 A 1.000** 3.482
710 R 1.000** 3.483
726 G 1.000** 3.483
730 L 0.789 2.958
735 L 0.999** 3.481
749 L 0.546 2.356
770 A 1.000** 3.483
771 W 1.000** 3.483
775 L 0.998** 3.478
776 H 0.694 2.724
785 L 0.990* 3.458
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: 01_AE.TH.06.98PB2.EU743784_)
Pr(w>1) post mean +- SE for w
10 W 1.000** 3.500 +- 0.012
15 T 0.989* 3.473 +- 0.261
73 Y 1.000** 3.500 +- 0.000
119 P 1.000** 3.500 +- 0.000
120 T 1.000** 3.500 +- 0.035
121 T 1.000** 3.500 +- 0.000
122 S 1.000** 3.500 +- 0.000
139 K 0.851 3.129 +- 0.889
140 Q 1.000** 3.500 +- 0.017
143 Y 0.985* 3.462 +- 0.304
155 N 0.994** 3.486 +- 0.189
156 K 1.000** 3.500 +- 0.003
157 T 1.000** 3.500 +- 0.000
158 T 1.000** 3.500 +- 0.001
168 V 0.998** 3.495 +- 0.106
177 S 0.513 2.283 +- 1.250
200 N 0.513 2.281 +- 1.250
208 N 0.990** 3.476 +- 0.246
249 T 0.949 3.372 +- 0.551
259 S 0.544 2.360 +- 1.245
261 Q 1.000** 3.500 +- 0.000
268 S 0.999** 3.496 +- 0.094
276 H 1.000** 3.500 +- 0.009
286 D 1.000** 3.500 +- 0.002
299 G 0.990** 3.476 +- 0.243
300 T 1.000** 3.500 +- 0.009
303 E 0.998** 3.495 +- 0.107
306 K 1.000** 3.500 +- 0.018
307 Q 1.000** 3.500 +- 0.000
309 A 1.000** 3.500 +- 0.017
310 K 1.000** 3.500 +- 0.000
313 K 1.000** 3.500 +- 0.007
315 H 0.755 2.888 +- 1.075
319 V 1.000** 3.500 +- 0.000
323 S 0.999** 3.498 +- 0.063
347 S 0.544 2.361 +- 1.245
348 Q 1.000** 3.500 +- 0.000
352 A 0.956* 3.389 +- 0.515
354 T 1.000** 3.500 +- 0.000
355 I 1.000** 3.500 +- 0.000
357 S 1.000** 3.500 +- 0.000
358 T 0.965* 3.412 +- 0.460
385 S 1.000** 3.500 +- 0.000
387 V 1.000** 3.500 +- 0.000
391 L 1.000** 3.500 +- 0.012
405 N 1.000** 3.500 +- 0.000
406 T 1.000** 3.500 +- 0.000
407 A 1.000** 3.500 +- 0.000
456 I 0.754 2.885 +- 1.076
548 A 1.000** 3.500 +- 0.024
553 S 0.999** 3.498 +- 0.067
560 Y 1.000** 3.500 +- 0.000
561 D 1.000** 3.500 +- 0.001
562 T 1.000** 3.500 +- 0.011
570 K 0.525 2.313 +- 1.248
576 S 0.658 2.645 +- 1.186
580 D 1.000** 3.500 +- 0.000
581 L 1.000** 3.500 +- 0.033
584 G 1.000** 3.500 +- 0.000
614 D 0.998** 3.496 +- 0.106
661 T 1.000** 3.500 +- 0.026
663 H 0.986* 3.465 +- 0.293
664 Q 0.890 3.226 +- 0.781
686 V 1.000** 3.500 +- 0.014
690 S 0.999** 3.498 +- 0.067
696 A 1.000** 3.499 +- 0.039
710 R 1.000** 3.500 +- 0.005
726 G 1.000** 3.500 +- 0.001
730 L 0.767 2.918 +- 1.056
735 L 0.999** 3.498 +- 0.077
749 L 0.515 2.288 +- 1.249
770 A 1.000** 3.500 +- 0.006
771 W 1.000** 3.500 +- 0.007
775 L 0.998** 3.494 +- 0.124
776 H 0.665 2.661 +- 1.180
785 L 0.988* 3.471 +- 0.269
Model 8 vs 7 1146.2362680000078
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 01_AE.TH.06.98PB2.EU743784_)
Pr(w>1) post mean +- SE for w
10 W 1.000** 3.021
15 T 0.990** 3.001
73 Y 1.000** 3.021
119 P 1.000** 3.021
120 T 1.000** 3.021
121 T 1.000** 3.021
122 S 1.000** 3.021
139 K 0.879 2.772
140 Q 1.000** 3.021
143 Y 0.987* 2.995
155 N 0.994** 3.009
156 K 1.000** 3.021
157 T 1.000** 3.021
158 T 1.000** 3.021
168 V 0.998** 3.018
177 S 0.647 2.280
200 N 0.597 2.185
208 N 0.991** 3.002
249 T 0.966* 2.950
259 S 0.669 2.332
261 Q 1.000** 3.021
268 S 0.998** 3.018
276 H 1.000** 3.021
286 D 1.000** 3.021
299 G 0.990** 3.001
300 T 1.000** 3.021
303 E 0.998** 3.017
306 K 1.000** 3.021
307 Q 1.000** 3.021
309 A 1.000** 3.021
310 K 1.000** 3.021
313 K 1.000** 3.021
315 H 0.806 2.618
319 V 1.000** 3.021
323 S 0.999** 3.020
347 S 0.689 2.371
348 Q 1.000** 3.021
352 A 0.956* 2.930
354 T 1.000** 3.021
355 I 1.000** 3.021
357 S 1.000** 3.021
358 T 0.972* 2.963
385 S 1.000** 3.021
387 V 1.000** 3.021
391 L 1.000** 3.021
405 N 1.000** 3.021
406 T 1.000** 3.021
407 A 1.000** 3.021
442 R 0.503 1.988
456 I 0.800 2.607
548 A 1.000** 3.021
553 S 0.999** 3.020
560 Y 1.000** 3.021
561 D 1.000** 3.021
562 T 1.000** 3.021
570 K 0.623 2.234
576 S 0.730 2.462
580 D 1.000** 3.021
581 L 1.000** 3.021
584 G 1.000** 3.021
614 D 0.998** 3.017
661 T 1.000** 3.021
663 H 0.989* 2.999
664 Q 0.926 2.866
686 V 1.000** 3.021
690 S 0.999** 3.019
696 A 1.000** 3.021
710 R 1.000** 3.021
726 G 1.000** 3.021
730 L 0.811 2.623
735 L 0.999** 3.019
749 L 0.628 2.246
770 A 1.000** 3.021
771 W 1.000** 3.021
775 L 0.998** 3.016
776 H 0.740 2.479
785 L 0.989* 2.999
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: 01_AE.TH.06.98PB2.EU743784_)
Pr(w>1) post mean +- SE for w
4 K 0.643 1.934 +- 0.761
10 W 1.000** 2.506 +- 0.079
15 T 0.998** 2.502 +- 0.108
73 Y 1.000** 2.506 +- 0.079
119 P 1.000** 2.506 +- 0.079
120 T 1.000** 2.506 +- 0.080
121 T 1.000** 2.506 +- 0.079
122 S 1.000** 2.506 +- 0.079
134 E 0.934 2.397 +- 0.391
139 K 0.985* 2.480 +- 0.197
140 Q 1.000** 2.506 +- 0.079
143 Y 0.997** 2.502 +- 0.111
153 P 0.904 2.349 +- 0.467
155 N 0.999** 2.505 +- 0.091
156 K 1.000** 2.506 +- 0.079
157 T 1.000** 2.506 +- 0.079
158 T 1.000** 2.506 +- 0.079
168 V 1.000** 2.505 +- 0.086
177 S 0.906 2.351 +- 0.471
200 N 0.947 2.417 +- 0.356
208 N 0.998** 2.504 +- 0.098
247 G 0.813 2.203 +- 0.620
249 T 0.994** 2.495 +- 0.144
251 T 0.529 1.747 +- 0.800
259 S 0.939 2.404 +- 0.383
261 Q 1.000** 2.506 +- 0.079
268 S 1.000** 2.506 +- 0.084
276 H 1.000** 2.506 +- 0.079
286 D 1.000** 2.506 +- 0.079
292 R 0.523 1.739 +- 0.798
294 Y 0.730 2.071 +- 0.707
299 G 0.999** 2.504 +- 0.097
300 T 1.000** 2.506 +- 0.079
302 N 0.873 2.301 +- 0.524
303 E 1.000** 2.506 +- 0.084
306 K 1.000** 2.506 +- 0.079
307 Q 1.000** 2.506 +- 0.079
309 A 1.000** 2.506 +- 0.079
310 K 1.000** 2.506 +- 0.079
313 K 1.000** 2.506 +- 0.079
315 H 0.965* 2.447 +- 0.296
319 V 1.000** 2.506 +- 0.079
323 S 1.000** 2.506 +- 0.084
347 S 0.939 2.405 +- 0.382
348 Q 1.000** 2.506 +- 0.079
352 A 0.993** 2.494 +- 0.144
354 T 1.000** 2.506 +- 0.079
355 I 1.000** 2.506 +- 0.079
357 S 1.000** 2.506 +- 0.079
358 T 0.995** 2.498 +- 0.132
374 G 0.858 2.276 +- 0.551
385 S 1.000** 2.506 +- 0.079
387 V 1.000** 2.506 +- 0.079
389 N 0.711 2.041 +- 0.722
391 L 1.000** 2.506 +- 0.079
405 N 1.000** 2.506 +- 0.079
406 T 1.000** 2.506 +- 0.079
407 A 1.000** 2.506 +- 0.079
409 T 0.776 2.145 +- 0.663
442 R 0.921 2.376 +- 0.427
456 I 0.965* 2.447 +- 0.296
459 M 0.881 2.312 +- 0.514
476 I 0.794 2.175 +- 0.639
548 A 1.000** 2.506 +- 0.079
553 S 1.000** 2.506 +- 0.082
560 Y 1.000** 2.506 +- 0.079
561 D 1.000** 2.506 +- 0.079
562 T 1.000** 2.506 +- 0.079
570 K 0.924 2.381 +- 0.422
576 S 0.970* 2.453 +- 0.272
580 D 1.000** 2.506 +- 0.079
581 L 1.000** 2.506 +- 0.080
584 G 1.000** 2.506 +- 0.079
586 L 0.533 1.751 +- 0.804
614 D 1.000** 2.506 +- 0.084
617 N 0.587 1.847 +- 0.780
661 T 1.000** 2.506 +- 0.080
663 H 0.998** 2.502 +- 0.109
664 Q 0.981* 2.475 +- 0.227
686 V 1.000** 2.506 +- 0.079
690 S 1.000** 2.506 +- 0.082
696 A 1.000** 2.506 +- 0.080
710 R 1.000** 2.506 +- 0.079
726 G 1.000** 2.506 +- 0.079
730 L 0.939 2.404 +- 0.392
735 L 1.000** 2.505 +- 0.086
739 Q 0.678 1.979 +- 0.759
749 L 0.930 2.390 +- 0.408
767 T 0.739 2.088 +- 0.695
770 A 1.000** 2.506 +- 0.079
771 W 1.000** 2.506 +- 0.079
775 L 0.999** 2.505 +- 0.092
776 H 0.953* 2.428 +- 0.337
785 L 0.997** 2.502 +- 0.112
