--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Jan 24 14:35:18 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_2/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -49154.63 -49198.77
2 -49157.06 -49202.12
--------------------------------------
TOTAL -49155.24 -49201.46
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/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} 10.796875 0.136484 10.066490 11.491960 10.783890 570.09 629.98 1.000
r(A<->C){all} 0.138577 0.000026 0.128762 0.148920 0.138385 365.99 472.84 1.000
r(A<->G){all} 0.297827 0.000119 0.276613 0.318814 0.297862 317.31 331.39 1.000
r(A<->T){all} 0.054101 0.000010 0.048338 0.060538 0.054072 526.53 556.54 1.000
r(C<->G){all} 0.074867 0.000026 0.065032 0.085095 0.074809 538.12 567.92 1.002
r(C<->T){all} 0.333263 0.000135 0.308496 0.353997 0.333251 284.83 328.04 1.000
r(G<->T){all} 0.101364 0.000023 0.091827 0.110989 0.101267 443.72 482.48 1.002
pi(A){all} 0.393346 0.000044 0.380242 0.405980 0.393338 405.66 439.69 1.001
pi(C){all} 0.177499 0.000024 0.168318 0.187267 0.177232 303.77 344.26 1.003
pi(G){all} 0.212677 0.000026 0.202237 0.222433 0.212612 345.06 388.18 1.000
pi(T){all} 0.216477 0.000033 0.205251 0.227226 0.216314 499.69 523.90 1.001
alpha{1,2} 0.467273 0.000469 0.423882 0.508041 0.466512 1035.98 1071.23 1.000
alpha{3} 0.998271 0.003814 0.885286 1.127218 0.996011 1120.47 1310.74 1.001
pinvar{all} 0.150933 0.000180 0.126376 0.177852 0.151186 980.60 1056.58 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 -38265.0987
Model 2: PositiveSelection -37739.443275
Model 0: one-ratio -40609.02207
Model 3: discrete -37698.212233
Model 7: beta -38081.391255
Model 8: beta&w>1 -37613.546788
Model 0 vs 1 4687.846739999994
Model 2 vs 1 1051.310850000009
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.NP.11.11NP014.KU341723_)
Pr(w>1) post mean +- SE for w
5 P 0.867 3.067
16 G 0.761 2.814
17 K 0.996** 3.374
69 V 1.000** 3.383
115 R 0.998** 3.377
116 N 0.995** 3.372
117 Y 1.000** 3.383
118 N 1.000** 3.383
119 V 1.000** 3.383
120 E 1.000** 3.383
129 A 0.592 2.412
132 E 0.960* 3.288
136 K 0.989* 3.356
144 L 0.994** 3.368
148 P 0.557 2.327
150 N 1.000** 3.383
151 S 1.000** 3.383
152 S 1.000** 3.383
153 E 1.000** 3.383
243 V 0.662 2.576
245 T 0.944 3.250
252 Q 1.000** 3.383
262 N 1.000** 3.383
270 R 1.000** 3.383
280 D 1.000** 3.383
293 R 0.587 2.399
296 E 1.000** 3.383
299 Q 1.000** 3.383
300 R 1.000** 3.383
302 G 1.000** 3.383
303 K 1.000** 3.383
306 A 0.976* 3.326
308 H 0.924 3.203
314 Q 1.000** 3.383
316 A 0.984* 3.345
317 S 0.999** 3.380
318 S 0.997** 3.376
343 G 1.000** 3.383
347 G 0.981* 3.339
348 N 0.998** 3.379
349 S 1.000** 3.383
350 T 1.000** 3.383
377 A 1.000** 3.382
379 E 1.000** 3.383
383 I 1.000** 3.383
396 P 1.000** 3.383
398 I 0.933 3.223
431 A 0.776 2.849
536 A 1.000** 3.383
541 S 1.000** 3.383
545 T 0.999** 3.381
546 Q 1.000** 3.383
547 S 1.000** 3.383
548 D 1.000** 3.383
551 D 0.993** 3.366
567 N 1.000** 3.383
568 T 1.000** 3.383
571 S 1.000** 3.383
601 D 1.000** 3.383
653 T 1.000** 3.382
657 S 1.000** 3.383
677 R 0.832 2.982
687 R 0.944 3.250
692 A 1.000** 3.383
701 Q 0.650 2.549
732 L 0.911 3.170
733 V 0.995** 3.370
736 L 1.000** 3.383
737 C 1.000** 3.383
741 R 0.978* 3.330
751 F 1.000** 3.382
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.NP.11.11NP014.KU341723_)
Pr(w>1) post mean +- SE for w
5 P 0.766 2.916 +- 1.058
16 G 0.579 2.446 +- 1.234
17 K 0.993** 3.481 +- 0.215
69 V 1.000** 3.500 +- 0.000
115 R 0.996** 3.489 +- 0.164
116 N 0.991** 3.476 +- 0.242
117 Y 1.000** 3.500 +- 0.000
118 N 1.000** 3.500 +- 0.000
119 V 1.000** 3.500 +- 0.000
120 E 1.000** 3.500 +- 0.004
132 E 0.920 3.301 +- 0.677
136 K 0.979* 3.447 +- 0.360
144 L 0.988* 3.471 +- 0.267
150 N 1.000** 3.500 +- 0.030
151 S 1.000** 3.500 +- 0.000
152 S 1.000** 3.500 +- 0.000
153 E 1.000** 3.500 +- 0.001
245 T 0.896 3.241 +- 0.762
252 Q 1.000** 3.500 +- 0.002
262 N 1.000** 3.500 +- 0.013
270 R 1.000** 3.500 +- 0.000
280 D 1.000** 3.500 +- 0.005
296 E 1.000** 3.500 +- 0.012
299 Q 1.000** 3.500 +- 0.002
300 R 1.000** 3.500 +- 0.003
302 G 1.000** 3.500 +- 0.000
303 K 1.000** 3.500 +- 0.012
306 A 0.949 3.373 +- 0.548
308 H 0.865 3.164 +- 0.853
314 Q 1.000** 3.500 +- 0.000
316 A 0.968* 3.421 +- 0.438
317 S 0.997** 3.493 +- 0.127
318 S 0.995** 3.488 +- 0.174
343 G 1.000** 3.500 +- 0.000
347 G 0.961* 3.402 +- 0.486
348 N 0.997** 3.493 +- 0.135
349 S 1.000** 3.500 +- 0.000
350 T 1.000** 3.500 +- 0.026
377 A 0.999** 3.498 +- 0.067
379 E 1.000** 3.500 +- 0.019
383 I 1.000** 3.499 +- 0.039
396 P 1.000** 3.500 +- 0.003
398 I 0.875 3.188 +- 0.826
431 A 0.620 2.550 +- 1.213
536 A 1.000** 3.500 +- 0.031
541 S 1.000** 3.500 +- 0.032
545 T 0.999** 3.496 +- 0.096
546 Q 1.000** 3.500 +- 0.003
547 S 1.000** 3.500 +- 0.000
548 D 1.000** 3.500 +- 0.000
551 D 0.985* 3.462 +- 0.305
567 N 1.000** 3.500 +- 0.000
568 T 1.000** 3.500 +- 0.010
571 S 1.000** 3.500 +- 0.000
601 D 1.000** 3.500 +- 0.001
653 T 1.000** 3.499 +- 0.051
657 S 1.000** 3.500 +- 0.001
677 R 0.730 2.826 +- 1.109
687 R 0.907 3.267 +- 0.727
692 A 1.000** 3.500 +- 0.031
701 Q 0.503 2.259 +- 1.250
732 L 0.832 3.080 +- 0.934
733 V 0.989* 3.474 +- 0.255
736 L 1.000** 3.500 +- 0.003
737 C 1.000** 3.500 +- 0.000
741 R 0.962* 3.406 +- 0.476
751 F 0.999** 3.499 +- 0.061
Model 8 vs 7 935.6889340000052
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.NP.11.11NP014.KU341723_)
Pr(w>1) post mean +- SE for w
5 P 0.875 2.631
16 G 0.778 2.445
17 K 0.994** 2.861
69 V 1.000** 2.873
115 R 0.997** 2.866
116 N 0.993** 2.860
117 Y 1.000** 2.873
118 N 1.000** 2.873
119 V 1.000** 2.873
120 E 1.000** 2.873
129 A 0.626 2.150
132 E 0.953* 2.783
136 K 0.985* 2.844
144 L 0.993** 2.859
148 P 0.605 2.108
150 N 1.000** 2.873
151 S 1.000** 2.873
152 S 1.000** 2.873
153 E 1.000** 2.873
243 V 0.736 2.358
245 T 0.949 2.774
252 Q 1.000** 2.873
262 N 1.000** 2.873
270 R 1.000** 2.873
280 D 1.000** 2.873
293 R 0.607 2.115
296 E 1.000** 2.873
299 Q 1.000** 2.873
300 R 1.000** 2.873
302 G 1.000** 2.873
303 K 1.000** 2.873
306 A 0.970* 2.815
308 H 0.922 2.722
314 Q 1.000** 2.873
316 A 0.978* 2.830
317 S 0.998** 2.869
318 S 0.997** 2.867
343 G 1.000** 2.873
347 G 0.976* 2.827
348 N 0.997** 2.867
349 S 1.000** 2.873
350 T 1.000** 2.873
377 A 0.999** 2.872
379 E 1.000** 2.873
383 I 1.000** 2.872
396 P 1.000** 2.873
398 I 0.941 2.758
431 A 0.793 2.472
536 A 1.000** 2.873
541 S 1.000** 2.873
545 T 0.999** 2.871
546 Q 1.000** 2.873
547 S 1.000** 2.873
548 D 1.000** 2.873
551 D 0.989* 2.852
567 N 1.000** 2.873
568 T 1.000** 2.873
571 S 1.000** 2.873
601 D 1.000** 2.873
653 T 1.000** 2.872
657 S 1.000** 2.873
663 A 0.513 1.920
677 R 0.868 2.615
687 R 0.953* 2.781
692 A 1.000** 2.873
701 Q 0.680 2.245
732 L 0.913 2.706
733 V 0.993** 2.860
736 L 1.000** 2.873
737 C 1.000** 2.873
741 R 0.981* 2.836
751 F 0.999** 2.872
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.NP.11.11NP014.KU341723_)
Pr(w>1) post mean +- SE for w
2 R 0.757 2.114 +- 0.683
4 R 0.537 1.755 +- 0.805
5 P 0.971* 2.454 +- 0.265
16 G 0.968* 2.450 +- 0.277
17 K 0.999** 2.498 +- 0.056
69 V 1.000** 2.500 +- 0.001
115 R 0.999** 2.498 +- 0.051
116 N 0.999** 2.498 +- 0.057
117 Y 1.000** 2.500 +- 0.001
118 N 1.000** 2.500 +- 0.001
119 V 1.000** 2.500 +- 0.001
120 E 1.000** 2.500 +- 0.002
129 A 0.930 2.390 +- 0.401
132 E 0.992** 2.487 +- 0.142
136 K 0.997** 2.495 +- 0.089
144 L 0.998** 2.497 +- 0.073
148 P 0.915 2.366 +- 0.441
150 N 1.000** 2.500 +- 0.011
151 S 1.000** 2.500 +- 0.001
152 S 1.000** 2.500 +- 0.001
153 E 1.000** 2.500 +- 0.001
163 A 0.587 1.834 +- 0.795
192 N 0.619 1.896 +- 0.770
239 L 0.796 2.171 +- 0.651
241 N 0.700 2.021 +- 0.733
243 V 0.931 2.390 +- 0.405
245 T 0.988* 2.481 +- 0.171
252 Q 1.000** 2.500 +- 0.002
262 N 1.000** 2.500 +- 0.006
270 R 1.000** 2.500 +- 0.001
280 D 1.000** 2.500 +- 0.003
293 R 0.937 2.401 +- 0.382
296 E 1.000** 2.500 +- 0.006
299 Q 1.000** 2.500 +- 0.002
300 R 1.000** 2.500 +- 0.002
302 G 1.000** 2.500 +- 0.001
303 K 1.000** 2.500 +- 0.006
306 A 0.995** 2.493 +- 0.107
308 H 0.980* 2.468 +- 0.223
314 Q 1.000** 2.500 +- 0.001
316 A 0.996** 2.493 +- 0.104
317 S 0.999** 2.499 +- 0.038
318 S 0.999** 2.498 +- 0.057
343 G 1.000** 2.500 +- 0.001
347 G 0.996** 2.494 +- 0.096
348 N 0.999** 2.499 +- 0.044
349 S 1.000** 2.500 +- 0.001
350 T 1.000** 2.500 +- 0.011
377 A 1.000** 2.500 +- 0.020
379 E 1.000** 2.500 +- 0.009
383 I 1.000** 2.500 +- 0.014
396 P 1.000** 2.500 +- 0.002
398 I 0.987* 2.479 +- 0.182
431 A 0.959* 2.435 +- 0.313
444 M 0.511 1.721 +- 0.798
517 K 0.599 1.860 +- 0.783
536 A 1.000** 2.500 +- 0.013
541 S 1.000** 2.500 +- 0.013
545 T 1.000** 2.499 +- 0.032
546 Q 1.000** 2.500 +- 0.003
547 S 1.000** 2.500 +- 0.001
548 D 1.000** 2.500 +- 0.001
551 D 0.998** 2.497 +- 0.067
563 S 0.764 2.126 +- 0.674
567 N 1.000** 2.500 +- 0.001
568 T 1.000** 2.500 +- 0.005
571 S 1.000** 2.500 +- 0.001
601 D 1.000** 2.500 +- 0.001
604 S 0.749 2.103 +- 0.688
653 T 1.000** 2.500 +- 0.022
657 S 1.000** 2.500 +- 0.001
663 A 0.840 2.244 +- 0.588
677 R 0.958* 2.433 +- 0.322
687 R 0.983* 2.473 +- 0.205
692 A 1.000** 2.500 +- 0.014
701 Q 0.886 2.317 +- 0.511
732 L 0.983* 2.473 +- 0.204
733 V 0.999** 2.498 +- 0.059
736 L 1.000** 2.500 +- 0.002
737 C 1.000** 2.500 +- 0.001
741 R 0.993** 2.489 +- 0.134
751 F 1.000** 2.500 +- 0.026
