--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Mar 15 01:46:38 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -48664.19 -48704.11
2 -48660.41 -48702.51
--------------------------------------
TOTAL -48661.08 -48703.60
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 7.870206 0.052154 7.441097 8.321572 7.870053 725.54 937.90 1.000
r(A<->C){all} 0.140204 0.000029 0.130070 0.150542 0.139982 359.83 400.53 1.000
r(A<->G){all} 0.293884 0.000122 0.272647 0.315905 0.293965 188.18 229.66 1.001
r(A<->T){all} 0.057949 0.000010 0.051737 0.063972 0.057912 515.89 534.92 1.002
r(C<->G){all} 0.075049 0.000025 0.066333 0.085532 0.074964 513.08 518.68 1.000
r(C<->T){all} 0.346683 0.000138 0.322485 0.368127 0.346471 213.59 254.69 1.000
r(G<->T){all} 0.086231 0.000019 0.078018 0.094919 0.086117 319.48 512.36 1.000
pi(A){all} 0.386740 0.000050 0.373746 0.401851 0.386734 210.01 306.33 1.000
pi(C){all} 0.171359 0.000025 0.161050 0.180935 0.171201 222.58 276.30 1.000
pi(G){all} 0.223939 0.000032 0.213688 0.236077 0.223881 286.80 398.06 1.000
pi(T){all} 0.217963 0.000034 0.206475 0.228823 0.218059 250.17 295.42 1.002
alpha{1,2} 0.526158 0.000651 0.476424 0.576596 0.525885 761.31 828.68 1.000
alpha{3} 1.140026 0.005302 1.004860 1.285954 1.137690 1501.00 1501.00 1.000
pinvar{all} 0.195264 0.000192 0.167768 0.220886 0.195251 672.47 836.32 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 -41627.237145
Model 2: PositiveSelection -40951.781415
Model 0: one-ratio -44297.988777
Model 3: discrete -40933.806577
Model 7: beta -41448.205743
Model 8: beta&w>1 -40858.949282
Model 0 vs 1 5341.503263999999
Model 2 vs 1 1350.911460000003
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.ZA.08.499_F5a.JQ777160_)
Pr(w>1) post mean +- SE for w
10 C 1.000** 3.419
12 Q 0.944 3.284
13 W 0.591 2.430
18 I 0.741 2.792
27 G 0.977* 3.364
79 H 1.000** 3.419
125 T 0.890 3.153
126 D 1.000** 3.419
127 N 1.000** 3.419
128 T 1.000** 3.419
137 A 1.000** 3.419
140 E 0.530 2.282
145 K 0.999** 3.417
148 T 0.994** 3.404
160 S 0.999** 3.417
161 N 1.000** 3.419
162 S 1.000** 3.419
163 E 0.978* 3.366
173 T 1.000** 3.419
182 T 0.961* 3.325
205 T 0.534 2.291
213 N 0.558 2.351
249 L 0.783 2.895
255 T 0.942 3.280
263 S 0.958* 3.318
265 P 1.000** 3.419
272 N 1.000** 3.419
280 R 0.995** 3.408
287 F 0.865 3.094
289 D 1.000** 3.419
304 S 1.000** 3.419
305 A 1.000** 3.419
308 K 1.000** 3.419
311 E 1.000** 3.419
312 R 1.000** 3.419
314 K 1.000** 3.419
315 K 1.000** 3.419
318 G 0.586 2.419
320 Y 0.650 2.573
326 D 1.000** 3.419
328 Q 0.987* 3.387
329 P 1.000** 3.419
330 A 0.956* 3.313
355 K 1.000** 3.419
361 N 0.997** 3.413
362 T 1.000** 3.419
363 E 1.000** 3.419
364 N 1.000** 3.419
365 N 1.000** 3.419
366 S 1.000** 3.419
367 T 0.849 3.053
394 A 1.000** 3.419
396 N 1.000** 3.419
400 V 1.000** 3.418
414 V 1.000** 3.419
415 N 1.000** 3.419
416 N 1.000** 3.419
417 N 1.000** 3.419
418 T 1.000** 3.419
453 E 0.996** 3.411
467 I 0.943 3.282
517 M 0.615 2.489
564 S 1.000** 3.419
570 S 0.629 2.523
571 I 1.000** 3.419
572 D 1.000** 3.419
573 E 1.000** 3.419
591 H 1.000** 3.419
592 T 1.000** 3.419
595 R 1.000** 3.419
625 N 1.000** 3.419
628 K 0.952* 3.304
671 L 0.954* 3.309
672 T 1.000** 3.419
674 N 1.000** 3.419
675 P 0.996** 3.411
697 I 1.000** 3.419
701 S 1.000** 3.418
730 T 0.608 2.470
743 T 1.000** 3.419
747 L 0.787 2.904
752 Q 0.989* 3.393
784 V 0.924 3.236
787 I 1.000** 3.419
788 F 1.000** 3.419
792 C 1.000** 3.419
802 F 0.993** 3.403
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.ZA.08.499_F5a.JQ777160_)
Pr(w>1) post mean +- SE for w
10 C 1.000** 3.500 +- 0.002
12 Q 0.944 3.360 +- 0.575
13 W 0.597 2.494 +- 1.226
18 I 0.734 2.836 +- 1.104
27 G 0.976* 3.440 +- 0.382
79 H 1.000** 3.500 +- 0.000
125 T 0.885 3.213 +- 0.797
126 D 1.000** 3.500 +- 0.024
127 N 1.000** 3.500 +- 0.000
128 T 1.000** 3.500 +- 0.000
137 A 1.000** 3.500 +- 0.009
140 E 0.506 2.265 +- 1.250
145 K 0.999** 3.498 +- 0.069
148 T 0.994** 3.485 +- 0.195
160 S 0.999** 3.498 +- 0.072
161 N 1.000** 3.500 +- 0.000
162 S 1.000** 3.500 +- 0.002
163 E 0.977* 3.444 +- 0.371
173 T 1.000** 3.500 +- 0.002
182 T 0.964* 3.410 +- 0.467
205 T 0.511 2.278 +- 1.250
213 N 0.540 2.350 +- 1.246
249 L 0.786 2.966 +- 1.024
255 T 0.941 3.354 +- 0.587
263 S 0.959* 3.398 +- 0.495
265 P 1.000** 3.500 +- 0.002
272 N 1.000** 3.500 +- 0.027
280 R 0.995** 3.489 +- 0.169
287 F 0.862 3.154 +- 0.863
289 D 1.000** 3.500 +- 0.001
304 S 1.000** 3.500 +- 0.000
305 A 1.000** 3.500 +- 0.001
308 K 1.000** 3.499 +- 0.040
311 E 1.000** 3.500 +- 0.001
312 R 1.000** 3.500 +- 0.000
314 K 1.000** 3.500 +- 0.020
315 K 1.000** 3.500 +- 0.001
318 G 0.561 2.403 +- 1.241
320 Y 0.644 2.609 +- 1.197
326 D 1.000** 3.500 +- 0.000
328 Q 0.986* 3.465 +- 0.296
329 P 1.000** 3.500 +- 0.017
330 A 0.959* 3.398 +- 0.493
355 K 1.000** 3.500 +- 0.000
361 N 0.998** 3.494 +- 0.124
362 T 1.000** 3.500 +- 0.000
363 E 1.000** 3.500 +- 0.000
364 N 1.000** 3.500 +- 0.006
365 N 1.000** 3.499 +- 0.040
366 S 1.000** 3.500 +- 0.000
367 T 0.844 3.110 +- 0.907
394 A 1.000** 3.500 +- 0.001
396 N 1.000** 3.500 +- 0.000
400 V 1.000** 3.499 +- 0.052
414 V 1.000** 3.500 +- 0.000
415 N 1.000** 3.500 +- 0.000
416 N 1.000** 3.500 +- 0.000
417 N 1.000** 3.500 +- 0.000
418 T 1.000** 3.500 +- 0.025
453 E 0.996** 3.491 +- 0.149
467 I 0.942 3.356 +- 0.583
517 M 0.625 2.562 +- 1.211
564 S 1.000** 3.500 +- 0.023
570 S 0.624 2.561 +- 1.211
571 I 1.000** 3.500 +- 0.000
572 D 1.000** 3.500 +- 0.003
573 E 1.000** 3.500 +- 0.006
591 H 1.000** 3.500 +- 0.000
592 T 1.000** 3.500 +- 0.009
595 R 1.000** 3.500 +- 0.000
625 N 1.000** 3.500 +- 0.009
628 K 0.950* 3.376 +- 0.544
671 L 0.956* 3.389 +- 0.514
672 T 1.000** 3.500 +- 0.000
674 N 1.000** 3.500 +- 0.001
675 P 0.997** 3.492 +- 0.141
697 I 1.000** 3.500 +- 0.003
701 S 1.000** 3.499 +- 0.049
730 T 0.595 2.488 +- 1.227
743 T 1.000** 3.500 +- 0.000
747 L 0.797 2.992 +- 1.006
752 Q 0.990** 3.475 +- 0.247
784 V 0.922 3.306 +- 0.669
787 I 1.000** 3.500 +- 0.001
788 F 1.000** 3.500 +- 0.000
792 C 1.000** 3.500 +- 0.004
802 F 0.994** 3.484 +- 0.199
Model 8 vs 7 1178.5129219999944
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.ZA.08.499_F5a.JQ777160_)
Pr(w>1) post mean +- SE for w
10 C 1.000** 2.969
12 Q 0.939 2.845
13 W 0.630 2.215
18 I 0.748 2.459
27 G 0.969* 2.907
79 H 1.000** 2.969
125 T 0.884 2.734
126 D 1.000** 2.968
127 N 1.000** 2.969
128 T 1.000** 2.969
137 A 1.000** 2.969
140 E 0.515 1.993
145 K 0.999** 2.967
148 T 0.992** 2.953
160 S 0.998** 2.966
161 N 1.000** 2.969
162 S 1.000** 2.969
163 E 0.972* 2.913
173 T 1.000** 2.969
182 T 0.966* 2.899
205 T 0.537 2.034
213 N 0.550 2.063
249 L 0.795 2.552
255 T 0.944 2.855
263 S 0.959* 2.887
265 P 1.000** 2.969
272 N 1.000** 2.968
280 R 0.993** 2.955
287 F 0.864 2.694
289 D 1.000** 2.969
304 S 1.000** 2.969
305 A 1.000** 2.969
308 K 0.999** 2.968
311 E 1.000** 2.969
312 R 1.000** 2.969
314 K 1.000** 2.968
315 K 1.000** 2.969
318 G 0.566 2.096
320 Y 0.657 2.274
326 D 1.000** 2.969
328 Q 0.979* 2.927
329 P 1.000** 2.969
330 A 0.962* 2.892
355 K 1.000** 2.969
361 N 0.997** 2.962
362 T 1.000** 2.969
363 E 1.000** 2.969
364 N 1.000** 2.969
365 N 0.999** 2.968
366 S 1.000** 2.969
367 T 0.845 2.656
394 A 1.000** 2.969
396 N 1.000** 2.969
400 V 0.999** 2.967
414 V 1.000** 2.969
415 N 1.000** 2.969
416 N 1.000** 2.969
417 N 1.000** 2.969
418 T 1.000** 2.968
453 E 0.995** 2.959
467 I 0.935 2.839
517 M 0.656 2.268
564 S 1.000** 2.968
570 S 0.678 2.316
571 I 1.000** 2.969
572 D 1.000** 2.969
573 E 1.000** 2.969
587 S 0.506 1.973
591 H 1.000** 2.969
592 T 1.000** 2.969
595 R 1.000** 2.969
625 N 1.000** 2.969
628 K 0.941 2.851
671 L 0.957* 2.882
672 T 1.000** 2.969
674 N 1.000** 2.969
675 P 0.996** 2.961
697 I 1.000** 2.969
701 S 0.999** 2.967
707 F 0.502 1.956
730 T 0.669 2.300
743 T 1.000** 2.969
747 L 0.797 2.554
752 Q 0.987* 2.942
784 V 0.919 2.806
787 I 1.000** 2.969
788 F 1.000** 2.969
792 C 1.000** 2.969
802 F 0.990** 2.949
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.ZA.08.499_F5a.JQ777160_)
Pr(w>1) post mean +- SE for w
7 K 0.691 2.009 +- 0.734
10 C 1.000** 2.500 +- 0.015
12 Q 0.987* 2.480 +- 0.179
13 W 0.887 2.320 +- 0.505
18 I 0.950* 2.422 +- 0.343
27 G 0.996** 2.494 +- 0.103
59 V 0.587 1.848 +- 0.778
79 H 1.000** 2.500 +- 0.015
125 T 0.982* 2.472 +- 0.210
126 D 1.000** 2.500 +- 0.018
127 N 1.000** 2.500 +- 0.015
128 T 1.000** 2.500 +- 0.015
137 A 1.000** 2.500 +- 0.016
140 E 0.921 2.377 +- 0.422
145 K 0.999** 2.499 +- 0.041
148 T 0.998** 2.497 +- 0.070
160 S 1.000** 2.500 +- 0.029
161 N 1.000** 2.500 +- 0.015
162 S 1.000** 2.500 +- 0.015
163 E 0.995** 2.493 +- 0.108
173 T 1.000** 2.500 +- 0.015
182 T 0.988* 2.482 +- 0.169
205 T 0.921 2.376 +- 0.424
211 P 0.569 1.818 +- 0.785
213 N 0.924 2.380 +- 0.417
249 L 0.947 2.416 +- 0.356
255 T 0.989* 2.483 +- 0.163
263 S 0.990** 2.485 +- 0.156
265 P 1.000** 2.500 +- 0.015
272 N 1.000** 2.500 +- 0.021
280 R 0.998** 2.498 +- 0.064
287 F 0.975* 2.461 +- 0.245
289 D 1.000** 2.500 +- 0.015
303 R 0.649 1.949 +- 0.750
304 S 1.000** 2.500 +- 0.015
305 A 1.000** 2.500 +- 0.015
308 K 1.000** 2.500 +- 0.023
311 E 1.000** 2.500 +- 0.015
312 R 1.000** 2.500 +- 0.015
314 K 1.000** 2.500 +- 0.019
315 K 1.000** 2.500 +- 0.015
318 G 0.937 2.402 +- 0.380
320 Y 0.926 2.383 +- 0.415
326 D 1.000** 2.500 +- 0.015
328 Q 0.997** 2.496 +- 0.083
329 P 1.000** 2.500 +- 0.018
330 A 0.987* 2.479 +- 0.181
355 K 1.000** 2.500 +- 0.015
361 N 0.999** 2.498 +- 0.061
362 T 1.000** 2.500 +- 0.015
363 E 1.000** 2.500 +- 0.015
364 N 1.000** 2.500 +- 0.016
365 N 1.000** 2.500 +- 0.023
366 S 1.000** 2.500 +- 0.015
367 T 0.973* 2.458 +- 0.254
394 A 1.000** 2.500 +- 0.015
396 N 1.000** 2.500 +- 0.015
400 V 1.000** 2.500 +- 0.027
414 V 1.000** 2.500 +- 0.015
415 N 1.000** 2.500 +- 0.015
416 N 1.000** 2.500 +- 0.015
417 N 1.000** 2.500 +- 0.015
418 T 1.000** 2.500 +- 0.022
453 E 0.999** 2.499 +- 0.054
467 I 0.989* 2.483 +- 0.165
487 I 0.731 2.077 +- 0.697
517 M 0.891 2.327 +- 0.496
559 N 0.835 2.241 +- 0.585
564 S 1.000** 2.500 +- 0.020
570 S 0.926 2.384 +- 0.413
571 I 1.000** 2.500 +- 0.015
572 D 1.000** 2.500 +- 0.015
573 E 1.000** 2.500 +- 0.016
587 S 0.925 2.382 +- 0.414
591 H 1.000** 2.500 +- 0.015
592 T 1.000** 2.500 +- 0.016
595 R 1.000** 2.500 +- 0.015
625 N 1.000** 2.500 +- 0.016
628 K 0.992** 2.487 +- 0.143
671 L 0.989* 2.482 +- 0.167
672 T 1.000** 2.500 +- 0.015
674 N 1.000** 2.500 +- 0.015
675 P 0.998** 2.498 +- 0.067
697 I 1.000** 2.500 +- 0.016
701 S 1.000** 2.500 +- 0.026
707 F 0.870 2.295 +- 0.532
709 D 0.634 1.921 +- 0.764
721 R 0.618 1.885 +- 0.784
730 T 0.936 2.399 +- 0.387
743 T 1.000** 2.500 +- 0.015
747 L 0.932 2.392 +- 0.401
752 Q 0.995** 2.492 +- 0.114
766 L 0.645 1.936 +- 0.762
783 I 0.755 2.114 +- 0.677
784 V 0.986* 2.479 +- 0.182
787 I 1.000** 2.500 +- 0.015
788 F 1.000** 2.500 +- 0.015
792 C 1.000** 2.500 +- 0.016
802 F 0.997** 2.496 +- 0.087
