--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Jan 26 22:08:29 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_N1/ENV_1_5/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -50178.64 -50224.08
2 -50179.17 -50220.14
--------------------------------------
TOTAL -50178.87 -50223.40
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/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} 10.502673 0.113840 9.911662 11.254180 10.489470 540.52 564.12 1.000
r(A<->C){all} 0.141198 0.000028 0.130787 0.151783 0.141111 350.49 481.77 1.002
r(A<->G){all} 0.289300 0.000094 0.271531 0.309303 0.289369 222.86 264.27 1.000
r(A<->T){all} 0.060100 0.000011 0.053249 0.065929 0.060004 518.94 535.03 1.000
r(C<->G){all} 0.075266 0.000026 0.065774 0.085408 0.075119 332.14 416.09 1.000
r(C<->T){all} 0.345880 0.000115 0.326707 0.368560 0.345459 217.80 246.73 1.000
r(G<->T){all} 0.088255 0.000021 0.079731 0.097180 0.088078 566.48 611.17 1.000
pi(A){all} 0.382923 0.000039 0.370105 0.394352 0.382881 331.65 382.85 1.000
pi(C){all} 0.172784 0.000023 0.162919 0.181803 0.172567 326.70 353.17 1.000
pi(G){all} 0.223296 0.000024 0.214625 0.233386 0.223227 295.07 330.66 1.000
pi(T){all} 0.220997 0.000031 0.210570 0.231729 0.221041 303.92 340.84 1.000
alpha{1,2} 0.446200 0.000386 0.408614 0.486364 0.445813 1015.32 1069.44 1.000
alpha{3} 1.031890 0.003635 0.918539 1.150164 1.031327 1105.13 1182.38 1.000
pinvar{all} 0.095988 0.000176 0.069434 0.120952 0.095957 979.26 993.45 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 -40904.63629
Model 2: PositiveSelection -40275.298151
Model 0: one-ratio -43299.134088
Model 3: discrete -40230.339606
Model 7: beta -40738.792083
Model 8: beta&w>1 -40146.38401
Model 0 vs 1 4788.995595999993
Model 2 vs 1 1258.676277999999
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.BW.96.96BW11B01.AF110971_)
Pr(w>1) post mean +- SE for w
18 G 0.587 2.468
51 V 0.729 2.824
71 V 1.000** 3.503
118 N 0.999** 3.500
119 T 1.000** 3.503
120 V 1.000** 3.503
121 N 1.000** 3.503
122 D 1.000** 3.503
123 T 1.000** 3.503
124 L 1.000** 3.503
125 H 1.000** 3.503
134 V 0.978* 3.447
140 R 0.804 3.013
142 Y 0.918 3.296
148 L 0.915 3.290
152 P 0.925 3.316
154 N 1.000** 3.503
155 N 1.000** 3.503
156 K 1.000** 3.503
157 E 1.000** 3.503
174 S 0.995** 3.490
203 N 1.000** 3.503
240 I 0.718 2.797
252 E 0.794 2.988
255 E 0.998** 3.499
262 N 0.872 3.182
270 R 1.000** 3.503
280 A 0.998** 3.498
294 E 1.000** 3.503
295 S 1.000** 3.503
296 Q 1.000** 3.503
299 N 0.980* 3.452
302 Q 1.000** 3.503
303 R 1.000** 3.503
305 S 1.000** 3.503
306 E 1.000** 3.503
309 K 0.864 3.162
311 H 0.929 3.324
317 K 1.000** 3.503
319 N 1.000** 3.502
320 Q 1.000** 3.503
321 P 1.000** 3.503
345 K 1.000** 3.503
346 Y 1.000** 3.503
347 I 1.000** 3.503
348 T 1.000** 3.503
375 A 1.000** 3.503
377 N 1.000** 3.503
381 K 1.000** 3.503
394 K 1.000** 3.503
395 N 1.000** 3.503
396 D 1.000** 3.503
428 K 0.997** 3.496
532 A 1.000** 3.502
537 A 0.983* 3.460
544 Q 1.000** 3.503
545 E 1.000** 3.503
546 E 0.999** 3.501
549 G 1.000** 3.503
565 D 1.000** 3.503
566 T 1.000** 3.503
569 R 1.000** 3.503
573 V 0.989* 3.476
599 D 1.000** 3.503
646 T 1.000** 3.503
648 N 0.696 2.743
649 P 0.533 2.335
671 I 1.000** 3.503
672 R 0.970* 3.427
675 S 0.645 2.614
681 A 1.000** 3.503
705 R 0.775 2.940
710 I 0.999** 3.500
719 Q 0.943 3.359
750 L 0.529 2.324
751 I 0.980* 3.453
754 I 0.997** 3.496
755 G 0.998** 3.497
759 R 0.733 2.834
769 F 0.995** 3.491
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.BW.96.96BW11B01.AF110971_)
Pr(w>1) post mean +- SE for w
18 G 0.678 2.695 +- 1.168
51 V 0.797 2.994 +- 1.005
71 V 1.000** 3.500 +- 0.001
118 N 0.999** 3.498 +- 0.071
119 T 1.000** 3.500 +- 0.013
120 V 1.000** 3.500 +- 0.000
121 N 1.000** 3.500 +- 0.000
122 D 1.000** 3.500 +- 0.001
123 T 1.000** 3.500 +- 0.000
124 L 1.000** 3.500 +- 0.000
125 H 1.000** 3.500 +- 0.000
134 V 0.984* 3.461 +- 0.309
140 R 0.857 3.142 +- 0.876
142 Y 0.941 3.353 +- 0.587
148 L 0.940 3.349 +- 0.596
152 P 0.947 3.368 +- 0.559
154 N 1.000** 3.500 +- 0.015
155 N 1.000** 3.500 +- 0.000
156 K 1.000** 3.500 +- 0.000
157 E 1.000** 3.500 +- 0.000
174 S 0.996** 3.491 +- 0.149
203 N 1.000** 3.500 +- 0.015
240 I 0.788 2.971 +- 1.021
252 E 0.849 3.123 +- 0.894
255 E 0.999** 3.497 +- 0.085
262 N 0.908 3.270 +- 0.723
270 R 1.000** 3.500 +- 0.002
280 A 0.999** 3.497 +- 0.089
294 E 1.000** 3.500 +- 0.001
295 S 1.000** 3.500 +- 0.000
296 Q 1.000** 3.500 +- 0.001
299 N 0.986* 3.464 +- 0.296
302 Q 1.000** 3.500 +- 0.002
303 R 1.000** 3.500 +- 0.000
305 S 1.000** 3.500 +- 0.000
306 E 1.000** 3.500 +- 0.000
309 K 0.902 3.255 +- 0.743
311 H 0.949 3.374 +- 0.548
317 K 1.000** 3.500 +- 0.000
319 N 1.000** 3.499 +- 0.039
320 Q 1.000** 3.500 +- 0.000
321 P 1.000** 3.500 +- 0.003
345 K 1.000** 3.500 +- 0.000
346 Y 1.000** 3.500 +- 0.001
347 I 1.000** 3.500 +- 0.000
348 T 1.000** 3.500 +- 0.003
375 A 1.000** 3.500 +- 0.003
377 N 1.000** 3.500 +- 0.000
381 K 1.000** 3.500 +- 0.006
394 K 1.000** 3.500 +- 0.000
395 N 1.000** 3.500 +- 0.000
396 D 1.000** 3.500 +- 0.000
428 K 0.998** 3.495 +- 0.106
532 A 1.000** 3.500 +- 0.024
537 A 0.988* 3.470 +- 0.271
544 Q 1.000** 3.500 +- 0.000
545 E 1.000** 3.500 +- 0.004
546 E 1.000** 3.499 +- 0.051
549 G 1.000** 3.500 +- 0.004
565 D 1.000** 3.500 +- 0.000
566 T 1.000** 3.500 +- 0.015
569 R 1.000** 3.500 +- 0.000
573 V 0.993** 3.481 +- 0.216
599 D 1.000** 3.500 +- 0.004
646 T 1.000** 3.500 +- 0.013
648 N 0.771 2.927 +- 1.051
649 P 0.629 2.572 +- 1.208
671 I 1.000** 3.500 +- 0.003
672 R 0.979* 3.446 +- 0.362
675 S 0.728 2.820 +- 1.112
681 A 1.000** 3.500 +- 0.004
705 R 0.834 3.085 +- 0.930
710 I 0.999** 3.498 +- 0.072
719 Q 0.959* 3.398 +- 0.494
750 L 0.625 2.563 +- 1.210
751 I 0.986* 3.465 +- 0.293
754 I 0.998** 3.495 +- 0.110
755 G 0.998** 3.496 +- 0.099
759 R 0.800 3.001 +- 0.999
769 F 0.997** 3.492 +- 0.142
Model 8 vs 7 1184.8161459999974
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.BW.96.96BW11B01.AF110971_)
Pr(w>1) post mean +- SE for w
18 G 0.819 2.598
51 V 0.879 2.721
71 V 1.000** 2.973
118 N 0.999** 2.971
119 T 1.000** 2.972
120 V 1.000** 2.973
121 N 1.000** 2.973
122 D 1.000** 2.973
123 T 1.000** 2.973
124 L 1.000** 2.973
125 H 1.000** 2.973
134 V 0.991** 2.954
140 R 0.913 2.792
142 Y 0.965* 2.901
148 L 0.960* 2.891
152 P 0.969* 2.909
154 N 1.000** 2.972
155 N 1.000** 2.973
156 K 1.000** 2.973
157 E 1.000** 2.973
174 S 0.998** 2.968
203 N 1.000** 2.972
240 I 0.853 2.665
252 E 0.918 2.803
253 S 0.608 2.152
255 E 0.999** 2.971
262 N 0.940 2.848
270 R 1.000** 2.973
280 A 0.999** 2.971
294 E 1.000** 2.973
295 S 1.000** 2.973
296 Q 1.000** 2.973
299 N 0.991** 2.954
302 Q 1.000** 2.973
303 R 1.000** 2.973
305 S 1.000** 2.973
306 E 1.000** 2.973
309 K 0.943 2.854
311 H 0.965* 2.901
317 K 1.000** 2.973
319 N 1.000** 2.972
320 Q 1.000** 2.973
321 P 1.000** 2.973
345 K 1.000** 2.973
346 Y 1.000** 2.973
347 I 1.000** 2.973
348 T 1.000** 2.973
375 A 1.000** 2.973
377 N 1.000** 2.973
381 K 1.000** 2.972
394 K 1.000** 2.973
395 N 1.000** 2.973
396 D 1.000** 2.973
428 K 0.999** 2.970
532 A 1.000** 2.972
537 A 0.992** 2.956
544 Q 1.000** 2.973
545 E 1.000** 2.973
546 E 1.000** 2.972
549 G 1.000** 2.973
565 D 1.000** 2.973
566 T 1.000** 2.972
569 R 1.000** 2.973
573 V 0.996** 2.963
599 D 1.000** 2.973
602 K 0.509 1.956
646 T 1.000** 2.972
648 N 0.856 2.673
649 P 0.733 2.413
671 I 1.000** 2.973
672 R 0.971* 2.913
675 S 0.829 2.620
681 A 1.000** 2.973
705 R 0.885 2.733
710 I 0.999** 2.971
719 Q 0.966* 2.902
750 L 0.754 2.464
751 I 0.992** 2.955
754 I 0.999** 2.970
755 G 0.999** 2.970
759 R 0.864 2.689
769 F 0.996** 2.965
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.BW.96.96BW11B01.AF110971_)
Pr(w>1) post mean +- SE for w
18 G 0.753 2.224 +- 0.805
48 E 0.542 1.790 +- 0.812
51 V 0.827 2.411 +- 0.778
71 V 1.000** 2.836 +- 0.472
118 N 0.999** 2.832 +- 0.477
119 T 1.000** 2.836 +- 0.472
120 V 1.000** 2.836 +- 0.472
121 N 1.000** 2.836 +- 0.472
122 D 1.000** 2.836 +- 0.472
123 T 1.000** 2.836 +- 0.472
124 L 1.000** 2.836 +- 0.472
125 H 1.000** 2.836 +- 0.472
134 V 0.971* 2.762 +- 0.558
140 R 0.866 2.507 +- 0.741
142 Y 0.953* 2.723 +- 0.605
148 L 0.940 2.691 +- 0.630
152 P 0.946 2.703 +- 0.617
154 N 1.000** 2.836 +- 0.472
155 N 1.000** 2.836 +- 0.472
156 K 1.000** 2.836 +- 0.472
157 E 1.000** 2.836 +- 0.472
174 S 0.997** 2.830 +- 0.482
203 N 1.000** 2.836 +- 0.472
240 I 0.847 2.478 +- 0.782
244 A 0.533 1.786 +- 0.851
252 E 0.853 2.469 +- 0.750
253 S 0.664 2.061 +- 0.881
255 E 0.998** 2.832 +- 0.477
262 N 0.908 2.610 +- 0.688
270 R 1.000** 2.836 +- 0.472
280 A 0.999** 2.833 +- 0.477
287 E 0.605 1.913 +- 0.832
294 E 1.000** 2.836 +- 0.472
295 S 1.000** 2.836 +- 0.472
296 Q 1.000** 2.836 +- 0.472
299 N 0.982* 2.791 +- 0.529
302 Q 1.000** 2.836 +- 0.472
303 R 1.000** 2.836 +- 0.472
305 S 1.000** 2.836 +- 0.472
306 E 1.000** 2.836 +- 0.472
309 K 0.896 2.579 +- 0.701
311 H 0.952* 2.720 +- 0.607
317 K 1.000** 2.836 +- 0.472
319 N 1.000** 2.835 +- 0.473
320 Q 1.000** 2.836 +- 0.472
321 P 1.000** 2.836 +- 0.472
345 K 1.000** 2.836 +- 0.472
346 Y 1.000** 2.836 +- 0.472
347 I 1.000** 2.836 +- 0.472
348 T 1.000** 2.836 +- 0.472
375 A 1.000** 2.836 +- 0.472
377 N 1.000** 2.836 +- 0.472
381 K 1.000** 2.836 +- 0.472
394 K 1.000** 2.836 +- 0.472
395 N 1.000** 2.836 +- 0.472
396 D 1.000** 2.836 +- 0.472
428 K 0.998** 2.831 +- 0.480
532 A 1.000** 2.836 +- 0.473
537 A 0.990* 2.812 +- 0.506
544 Q 1.000** 2.836 +- 0.472
545 E 1.000** 2.836 +- 0.472
546 E 0.999** 2.835 +- 0.474
549 G 1.000** 2.836 +- 0.472
561 S 0.505 1.725 +- 0.809
565 D 1.000** 2.836 +- 0.472
566 T 1.000** 2.836 +- 0.472
569 R 1.000** 2.836 +- 0.472
573 V 0.989* 2.809 +- 0.507
599 D 1.000** 2.836 +- 0.472
602 K 0.617 1.932 +- 0.820
646 T 1.000** 2.836 +- 0.472
648 N 0.829 2.425 +- 0.788
649 P 0.757 2.276 +- 0.863
671 I 1.000** 2.836 +- 0.472
672 R 0.974* 2.781 +- 0.559
675 S 0.772 2.275 +- 0.806
681 A 1.000** 2.836 +- 0.472
695 R 0.556 1.842 +- 0.886
705 R 0.881 2.560 +- 0.742
710 I 0.999** 2.834 +- 0.475
719 Q 0.962* 2.748 +- 0.586
733 L 0.536 1.793 +- 0.868
750 L 0.737 2.199 +- 0.825
751 I 0.984* 2.797 +- 0.522
754 I 0.998** 2.831 +- 0.479
755 G 0.999** 2.833 +- 0.477
759 R 0.857 2.499 +- 0.770
769 F 0.996** 2.827 +- 0.486
