--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Jan 25 09:11:05 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -47535.55 -47579.59
2 -47533.27 -47573.31
--------------------------------------
TOTAL -47533.87 -47578.89
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 8.147714 0.052385 7.729361 8.626980 8.139656 1076.76 1204.17 1.001
r(A<->C){all} 0.141654 0.000032 0.130391 0.152396 0.141447 401.70 411.87 1.000
r(A<->G){all} 0.291887 0.000102 0.272137 0.311162 0.291604 145.65 180.29 1.000
r(A<->T){all} 0.046725 0.000008 0.041422 0.052354 0.046612 323.12 464.97 1.000
r(C<->G){all} 0.075533 0.000024 0.066197 0.084946 0.075400 553.00 591.86 1.001
r(C<->T){all} 0.357902 0.000122 0.336487 0.379274 0.357698 160.72 168.28 1.000
r(G<->T){all} 0.086299 0.000022 0.076782 0.095107 0.086236 423.94 451.99 1.002
pi(A){all} 0.399936 0.000045 0.386726 0.412288 0.399934 290.39 292.73 1.000
pi(C){all} 0.165861 0.000024 0.156395 0.175030 0.165837 179.73 242.44 1.000
pi(G){all} 0.218510 0.000027 0.208984 0.228663 0.218562 292.20 298.88 1.000
pi(T){all} 0.215693 0.000035 0.204815 0.227487 0.215640 227.78 310.02 1.000
alpha{1,2} 0.477318 0.000529 0.433189 0.524312 0.476482 997.07 1084.58 1.000
alpha{3} 1.126482 0.004631 0.993516 1.259227 1.126366 1182.96 1268.03 1.000
pinvar{all} 0.195947 0.000190 0.169324 0.221458 0.195847 1151.71 1168.68 1.001
------------------------------------------------------------------------------------------------------
* 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 -39250.562022
Model 2: PositiveSelection -38585.194973
Model 0: one-ratio -41788.41876
Model 3: discrete -38541.392658
Model 7: beta -39026.033037
Model 8: beta&w>1 -38448.428616
Model 0 vs 1 5075.713476000004
Model 2 vs 1 1330.7340980000008
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.03.03ZAPS133MB1.DQ275646_)
Pr(w>1) post mean +- SE for w
4 K 0.981* 3.536
7 Q 0.846 3.186
14 M 0.976* 3.523
55 E 0.956* 3.471
78 V 1.000** 3.584
125 T 1.000** 3.584
127 A 1.000** 3.584
135 T 0.999** 3.581
142 K 1.000** 3.583
145 Y 0.559 2.445
155 P 0.996** 3.573
157 N 1.000** 3.584
158 G 1.000** 3.584
159 N 1.000** 3.584
160 S 1.000** 3.584
179 S 0.897 3.317
246 L 0.878 3.268
260 S 0.938 3.423
262 Q 1.000** 3.584
264 V 0.997** 3.577
277 R 1.000** 3.584
299 D 1.000** 3.584
300 Q 0.998** 3.578
303 R 0.745 2.925
306 E 1.000** 3.584
307 Q 1.000** 3.584
309 K 1.000** 3.584
310 K 1.000** 3.584
313 G 1.000** 3.584
315 H 0.999** 3.580
319 L 1.000** 3.584
321 A 1.000** 3.584
322 P 0.987* 3.550
323 A 1.000** 3.584
348 N 1.000** 3.584
351 K 1.000** 3.584
352 S 1.000** 3.584
353 D 1.000** 3.583
354 E 1.000** 3.584
382 E 1.000** 3.583
384 N 1.000** 3.584
386 T 0.680 2.756
388 N 1.000** 3.584
402 R 1.000** 3.584
403 N 1.000** 3.583
404 D 1.000** 3.584
405 T 1.000** 3.584
440 T 0.796 3.058
544 A 1.000** 3.583
549 S 1.000** 3.583
555 Q 1.000** 3.584
556 T 1.000** 3.584
557 D 1.000** 3.583
560 D 1.000** 3.584
572 N 0.872 3.252
576 G 1.000** 3.584
577 T 1.000** 3.584
580 R 1.000** 3.584
610 D 0.987* 3.551
657 T 1.000** 3.584
659 N 1.000** 3.583
660 P 0.995** 3.570
682 V 1.000** 3.583
686 S 0.959* 3.477
692 A 1.000** 3.584
719 H 0.999** 3.582
724 A 1.000** 3.583
733 Q 0.868 3.241
760 V 0.991** 3.560
761 I 0.855 3.209
764 I 0.990* 3.557
765 C 1.000** 3.584
769 S 1.000** 3.584
779 F 0.985* 3.545
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.03.03ZAPS133MB1.DQ275646_)
Pr(w>1) post mean +- SE for w
4 K 0.981* 3.454 +- 0.338
7 Q 0.845 3.112 +- 0.905
14 M 0.975* 3.438 +- 0.388
55 E 0.957* 3.392 +- 0.508
78 V 1.000** 3.500 +- 0.001
125 T 1.000** 3.500 +- 0.012
127 A 1.000** 3.500 +- 0.000
135 T 0.999** 3.498 +- 0.078
142 K 1.000** 3.499 +- 0.050
145 Y 0.581 2.452 +- 1.234
155 P 0.995** 3.489 +- 0.168
157 N 1.000** 3.500 +- 0.007
158 G 1.000** 3.500 +- 0.000
159 N 1.000** 3.500 +- 0.001
160 S 1.000** 3.500 +- 0.000
179 S 0.892 3.229 +- 0.777
246 L 0.870 3.176 +- 0.839
260 S 0.935 3.338 +- 0.615
262 Q 1.000** 3.500 +- 0.005
264 V 0.997** 3.493 +- 0.133
277 R 1.000** 3.500 +- 0.001
299 D 1.000** 3.500 +- 0.000
300 Q 0.998** 3.495 +- 0.114
303 R 0.763 2.909 +- 1.062
306 E 1.000** 3.500 +- 0.000
307 Q 1.000** 3.500 +- 0.000
309 K 1.000** 3.500 +- 0.000
310 K 1.000** 3.500 +- 0.000
313 G 1.000** 3.500 +- 0.018
315 H 0.999** 3.497 +- 0.093
319 L 1.000** 3.500 +- 0.000
321 A 1.000** 3.500 +- 0.006
322 P 0.986* 3.466 +- 0.290
323 A 1.000** 3.500 +- 0.007
348 N 1.000** 3.500 +- 0.001
351 K 1.000** 3.500 +- 0.000
352 S 1.000** 3.500 +- 0.000
353 D 1.000** 3.499 +- 0.043
354 E 1.000** 3.500 +- 0.000
382 E 1.000** 3.500 +- 0.026
384 N 1.000** 3.500 +- 0.000
386 T 0.702 2.756 +- 1.143
388 N 1.000** 3.500 +- 0.011
402 R 1.000** 3.500 +- 0.000
403 N 1.000** 3.500 +- 0.031
404 D 1.000** 3.500 +- 0.000
405 T 1.000** 3.500 +- 0.004
440 T 0.806 3.015 +- 0.989
544 A 1.000** 3.500 +- 0.020
549 S 1.000** 3.499 +- 0.045
555 Q 1.000** 3.500 +- 0.000
556 T 1.000** 3.500 +- 0.000
557 D 1.000** 3.499 +- 0.043
560 D 1.000** 3.500 +- 0.010
572 N 0.879 3.197 +- 0.816
576 G 1.000** 3.500 +- 0.000
577 T 1.000** 3.500 +- 0.001
580 R 1.000** 3.500 +- 0.000
610 D 0.987* 3.468 +- 0.279
657 T 1.000** 3.500 +- 0.000
659 N 1.000** 3.500 +- 0.034
660 P 0.994** 3.485 +- 0.191
682 V 1.000** 3.499 +- 0.050
686 S 0.959* 3.397 +- 0.496
692 A 1.000** 3.500 +- 0.013
719 H 0.999** 3.498 +- 0.073
724 A 1.000** 3.499 +- 0.051
733 Q 0.860 3.151 +- 0.867
760 V 0.990** 3.476 +- 0.243
761 I 0.858 3.145 +- 0.872
764 I 0.989* 3.473 +- 0.260
765 C 1.000** 3.500 +- 0.000
769 S 1.000** 3.500 +- 0.014
779 F 0.984* 3.460 +- 0.313
Model 8 vs 7 1155.2088420000073
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.03.03ZAPS133MB1.DQ275646_)
Pr(w>1) post mean +- SE for w
4 K 0.977* 3.015
7 Q 0.850 2.744
14 M 0.975* 3.010
55 E 0.949 2.954
78 V 1.000** 3.062
125 T 1.000** 3.062
127 A 1.000** 3.062
135 T 0.998** 3.059
142 K 0.999** 3.061
145 Y 0.605 2.223
155 P 0.994** 3.050
157 N 1.000** 3.062
158 G 1.000** 3.062
159 N 1.000** 3.062
160 S 1.000** 3.062
179 S 0.916 2.884
246 L 0.887 2.821
260 S 0.945 2.946
262 Q 1.000** 3.062
264 V 0.995** 3.051
277 R 1.000** 3.062
299 D 1.000** 3.062
300 Q 0.996** 3.054
303 R 0.721 2.474
306 E 1.000** 3.062
307 Q 1.000** 3.062
309 K 1.000** 3.062
310 K 1.000** 3.062
313 G 1.000** 3.062
315 H 0.998** 3.059
319 L 1.000** 3.062
321 A 1.000** 3.062
322 P 0.984* 3.028
323 A 1.000** 3.062
348 N 1.000** 3.062
351 K 1.000** 3.062
352 S 1.000** 3.062
353 D 0.999** 3.061
354 E 1.000** 3.062
382 E 1.000** 3.062
384 N 1.000** 3.062
386 T 0.647 2.316
388 N 1.000** 3.062
402 R 1.000** 3.062
403 N 1.000** 3.062
404 D 1.000** 3.062
405 T 1.000** 3.062
440 T 0.801 2.641
544 A 1.000** 3.062
549 S 1.000** 3.062
555 Q 1.000** 3.062
556 T 1.000** 3.062
557 D 0.999** 3.061
560 D 1.000** 3.062
572 N 0.856 2.758
576 G 1.000** 3.062
577 T 1.000** 3.062
580 R 1.000** 3.062
610 D 0.983* 3.027
657 T 1.000** 3.062
659 N 1.000** 3.062
660 P 0.994** 3.050
682 V 0.999** 3.061
686 S 0.953* 2.962
692 A 1.000** 3.062
719 H 0.999** 3.060
724 A 1.000** 3.061
733 Q 0.867 2.778
760 V 0.988* 3.038
761 I 0.845 2.736
764 I 0.988* 3.037
765 C 1.000** 3.062
769 S 1.000** 3.062
779 F 0.981* 3.022
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.03.03ZAPS133MB1.DQ275646_)
Pr(w>1) post mean +- SE for w
4 K 0.841 3.092 +- 0.936
14 M 0.865 3.155 +- 0.874
55 E 0.681 2.682 +- 1.193
78 V 1.000** 3.499 +- 0.023
125 T 1.000** 3.499 +- 0.038
127 A 1.000** 3.499 +- 0.023
135 T 0.989* 3.471 +- 0.271
142 K 0.995** 3.487 +- 0.178
155 P 0.967* 3.415 +- 0.458
157 N 1.000** 3.499 +- 0.034
158 G 1.000** 3.499 +- 0.023
159 N 1.000** 3.499 +- 0.023
160 S 1.000** 3.499 +- 0.023
179 S 0.680 2.678 +- 1.198
246 L 0.620 2.524 +- 1.247
260 S 0.745 2.844 +- 1.118
262 Q 1.000** 3.499 +- 0.027
264 V 0.967* 3.415 +- 0.458
277 R 1.000** 3.499 +- 0.023
299 D 1.000** 3.499 +- 0.023
300 Q 0.975* 3.436 +- 0.399
306 E 1.000** 3.499 +- 0.023
307 Q 1.000** 3.499 +- 0.023
309 K 1.000** 3.499 +- 0.023
310 K 1.000** 3.499 +- 0.023
313 G 1.000** 3.498 +- 0.056
315 H 0.993** 3.481 +- 0.217
319 L 1.000** 3.499 +- 0.023
321 A 1.000** 3.499 +- 0.029
322 P 0.904 3.254 +- 0.754
323 A 1.000** 3.499 +- 0.025
348 N 1.000** 3.499 +- 0.023
351 K 1.000** 3.499 +- 0.023
352 S 1.000** 3.499 +- 0.023
353 D 0.996** 3.489 +- 0.167
354 E 1.000** 3.499 +- 0.023
382 E 0.999** 3.497 +- 0.084
384 N 1.000** 3.499 +- 0.023
388 N 1.000** 3.499 +- 0.035
402 R 1.000** 3.499 +- 0.023
403 N 0.999** 3.496 +- 0.097
404 D 1.000** 3.499 +- 0.023
405 T 1.000** 3.499 +- 0.025
544 A 1.000** 3.499 +- 0.049
549 S 0.999** 3.497 +- 0.090
555 Q 1.000** 3.499 +- 0.023
556 T 1.000** 3.499 +- 0.023
557 D 0.997** 3.493 +- 0.130
560 D 1.000** 3.499 +- 0.043
576 G 1.000** 3.499 +- 0.023
577 T 1.000** 3.499 +- 0.023
580 R 1.000** 3.499 +- 0.023
610 D 0.875 3.180 +- 0.845
657 T 1.000** 3.499 +- 0.023
659 N 0.999** 3.498 +- 0.074
660 P 0.979* 3.446 +- 0.367
682 V 0.997** 3.493 +- 0.134
686 S 0.702 2.736 +- 1.171
692 A 1.000** 3.499 +- 0.033
719 H 0.997** 3.493 +- 0.132
724 A 0.999** 3.496 +- 0.095
733 Q 0.561 2.371 +- 1.275
760 V 0.929 3.318 +- 0.656
764 I 0.928 3.315 +- 0.661
765 C 1.000** 3.499 +- 0.023
769 S 1.000** 3.499 +- 0.032
779 F 0.903 3.251 +- 0.758
