--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Jan 23 23:07:50 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_1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -46829.37 -46875.01
2 -46826.96 -46876.45
--------------------------------------
TOTAL -46827.56 -46875.97
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/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_N1/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} 7.835093 0.048588 7.388076 8.258520 7.824838 522.49 825.16 1.000
r(A<->C){all} 0.145315 0.000033 0.133576 0.156111 0.145293 292.97 387.22 1.002
r(A<->G){all} 0.265284 0.000129 0.242404 0.285663 0.265236 140.54 164.14 1.001
r(A<->T){all} 0.049455 0.000008 0.043833 0.054798 0.049446 496.19 531.48 1.001
r(C<->G){all} 0.072205 0.000027 0.062387 0.082184 0.072172 564.30 571.35 1.000
r(C<->T){all} 0.383739 0.000164 0.358880 0.407808 0.383664 156.16 170.13 1.002
r(G<->T){all} 0.084002 0.000021 0.075477 0.093131 0.083938 330.98 390.68 1.000
pi(A){all} 0.400853 0.000044 0.386580 0.412449 0.400805 448.81 451.16 1.000
pi(C){all} 0.155870 0.000023 0.146719 0.165009 0.155762 260.32 329.84 1.000
pi(G){all} 0.230024 0.000044 0.216906 0.242461 0.230151 151.41 191.22 1.000
pi(T){all} 0.213254 0.000038 0.200874 0.224933 0.213144 303.53 310.06 1.000
alpha{1,2} 0.455799 0.000507 0.412984 0.500649 0.454861 671.52 726.63 1.001
alpha{3} 1.000879 0.003938 0.879968 1.121255 0.997946 982.20 1080.37 1.000
pinvar{all} 0.182920 0.000234 0.151893 0.211025 0.182903 889.89 898.39 1.002
------------------------------------------------------------------------------------------------------
* 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 -39499.780509
Model 2: PositiveSelection -38800.288381
Model 0: one-ratio -42177.068401
Model 3: discrete -38772.241635
Model 7: beta -39306.355662
Model 8: beta&w>1 -38679.867436
Model 0 vs 1 5354.575784000001
Model 2 vs 1 1398.984255999996
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.CAP327.2.00_C6.37.KF114885_)
Pr(w>1) post mean +- SE for w
7 L 1.000** 3.633
10 W 1.000** 3.633
12 Q 0.990** 3.607
24 N 0.566 2.490
76 V 1.000** 3.633
122 T 1.000** 3.633
124 A 1.000** 3.633
125 N 1.000** 3.633
126 L 1.000** 3.633
127 K 1.000** 3.633
128 E 1.000** 3.633
141 Q 1.000** 3.633
143 Y 0.776 3.043
153 P 0.883 3.325
155 N 0.999** 3.630
156 Y 1.000** 3.633
157 S 1.000** 3.633
158 E 1.000** 3.633
177 T 0.990** 3.608
208 H 0.994** 3.617
245 L 0.928 3.445
247 D 0.703 2.852
249 A 0.980* 3.582
259 S 0.946 3.490
261 E 0.977* 3.573
268 D 1.000** 3.633
286 N 0.999** 3.632
300 K 0.998** 3.628
301 G 1.000** 3.633
305 T 0.983* 3.589
308 K 1.000** 3.633
309 R 1.000** 3.633
311 E 0.979* 3.579
312 K 1.000** 3.633
315 K 0.999** 3.631
322 N 1.000** 3.633
324 A 1.000** 3.633
325 P 1.000** 3.633
326 P 1.000** 3.633
351 E 1.000** 3.633
355 T 0.665 2.752
356 S 1.000** 3.633
357 E 1.000** 3.633
358 L 1.000** 3.633
360 K 1.000** 3.633
361 T 0.999** 3.632
377 E 0.985* 3.593
388 A 1.000** 3.633
394 V 1.000** 3.633
408 N 1.000** 3.633
409 N 1.000** 3.633
410 N 1.000** 3.633
411 N 1.000** 3.633
412 N 1.000** 3.633
447 Q 1.000** 3.633
553 N 1.000** 3.633
558 S 0.999** 3.632
565 D 1.000** 3.633
568 D 1.000** 3.633
584 D 1.000** 3.633
588 K 1.000** 3.633
618 D 1.000** 3.633
665 I 1.000** 3.633
667 N 0.767 3.020
668 P 0.996** 3.623
687 N 0.920 3.422
690 I 1.000** 3.633
691 R 0.585 2.539
694 N 0.981* 3.583
700 A 0.988* 3.602
714 Q 0.999** 3.630
732 A 1.000** 3.633
776 I 1.000** 3.633
777 C 1.000** 3.633
781 L 1.000** 3.633
791 F 0.639 2.683
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.CAP327.2.00_C6.37.KF114885_)
Pr(w>1) post mean +- SE for w
7 L 1.000** 3.499 +- 0.038
10 W 1.000** 3.500 +- 0.000
12 Q 0.991** 3.479 +- 0.231
24 N 0.659 2.647 +- 1.185
76 V 1.000** 3.500 +- 0.005
122 T 1.000** 3.500 +- 0.017
124 A 1.000** 3.500 +- 0.000
125 N 1.000** 3.500 +- 0.000
126 L 1.000** 3.500 +- 0.000
127 K 1.000** 3.500 +- 0.000
128 E 1.000** 3.499 +- 0.041
141 Q 1.000** 3.500 +- 0.011
143 Y 0.823 3.058 +- 0.954
153 P 0.913 3.283 +- 0.704
155 N 0.999** 3.497 +- 0.087
156 Y 1.000** 3.500 +- 0.000
157 S 1.000** 3.500 +- 0.001
158 E 1.000** 3.500 +- 0.000
177 T 0.991** 3.477 +- 0.237
208 H 0.995** 3.487 +- 0.182
245 L 0.937 3.343 +- 0.606
247 D 0.776 2.939 +- 1.043
249 A 0.984* 3.460 +- 0.315
259 S 0.955* 3.387 +- 0.519
261 E 0.984* 3.460 +- 0.315
268 D 1.000** 3.500 +- 0.004
286 N 1.000** 3.499 +- 0.051
300 K 0.999** 3.496 +- 0.096
301 G 1.000** 3.500 +- 0.000
305 T 0.987* 3.468 +- 0.281
308 K 1.000** 3.500 +- 0.014
309 R 1.000** 3.500 +- 0.028
311 E 0.983* 3.458 +- 0.320
312 K 1.000** 3.500 +- 0.004
315 K 0.999** 3.498 +- 0.070
322 N 1.000** 3.500 +- 0.001
324 A 1.000** 3.500 +- 0.003
325 P 1.000** 3.500 +- 0.003
326 P 1.000** 3.499 +- 0.038
351 E 1.000** 3.500 +- 0.001
355 T 0.754 2.886 +- 1.076
356 S 1.000** 3.500 +- 0.000
357 E 1.000** 3.500 +- 0.000
358 L 1.000** 3.500 +- 0.000
360 K 1.000** 3.500 +- 0.000
361 T 0.999** 3.499 +- 0.056
377 E 0.989* 3.471 +- 0.266
388 A 1.000** 3.500 +- 0.017
394 V 1.000** 3.500 +- 0.002
408 N 1.000** 3.500 +- 0.000
409 N 1.000** 3.500 +- 0.000
410 N 1.000** 3.500 +- 0.000
411 N 1.000** 3.500 +- 0.000
412 N 1.000** 3.500 +- 0.002
447 Q 1.000** 3.500 +- 0.024
534 K 0.506 2.265 +- 1.250
553 N 1.000** 3.500 +- 0.000
558 S 0.999** 3.499 +- 0.058
565 D 1.000** 3.500 +- 0.000
568 D 1.000** 3.500 +- 0.003
584 D 1.000** 3.500 +- 0.000
588 K 1.000** 3.499 +- 0.041
618 D 1.000** 3.500 +- 0.000
665 I 1.000** 3.500 +- 0.015
667 N 0.817 3.044 +- 0.966
668 P 0.996** 3.491 +- 0.154
687 N 0.939 3.349 +- 0.596
690 I 1.000** 3.500 +- 0.012
691 R 0.626 2.566 +- 1.209
694 N 0.985* 3.463 +- 0.302
700 A 0.989* 3.474 +- 0.256
714 Q 0.999** 3.497 +- 0.090
732 A 1.000** 3.500 +- 0.015
776 I 1.000** 3.500 +- 0.033
777 C 1.000** 3.500 +- 0.000
781 L 1.000** 3.500 +- 0.005
791 F 0.698 2.746 +- 1.148
Model 8 vs 7 1252.9764520000026
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.CAP327.2.00_C6.37.KF114885_)
Pr(w>1) post mean +- SE for w
7 L 1.000** 3.159
10 W 1.000** 3.160
12 Q 0.989* 3.136
24 N 0.595 2.264
76 V 1.000** 3.159
122 T 1.000** 3.159
124 A 1.000** 3.160
125 N 1.000** 3.160
126 L 1.000** 3.160
127 K 1.000** 3.160
128 E 0.999** 3.158
141 Q 1.000** 3.159
143 Y 0.805 2.726
153 P 0.892 2.922
155 N 0.998** 3.154
156 Y 1.000** 3.160
157 S 1.000** 3.160
158 E 1.000** 3.160
177 T 0.991** 3.140
208 H 0.993** 3.143
245 L 0.933 3.011
247 D 0.709 2.518
249 A 0.983* 3.122
259 S 0.954* 3.058
261 E 0.972* 3.097
268 D 1.000** 3.160
286 N 0.999** 3.158
300 K 0.997** 3.153
301 G 1.000** 3.160
305 T 0.980* 3.114
308 K 1.000** 3.159
309 R 1.000** 3.159
311 E 0.979* 3.113
312 K 1.000** 3.159
315 K 0.998** 3.156
322 N 1.000** 3.160
324 A 1.000** 3.160
325 P 1.000** 3.160
326 P 1.000** 3.159
351 E 1.000** 3.160
355 T 0.671 2.433
356 S 1.000** 3.160
357 E 1.000** 3.160
358 L 1.000** 3.160
360 K 1.000** 3.160
361 T 0.999** 3.158
377 E 0.983* 3.122
388 A 1.000** 3.159
394 V 1.000** 3.160
408 N 1.000** 3.160
409 N 1.000** 3.160
410 N 1.000** 3.160
411 N 1.000** 3.160
412 N 1.000** 3.160
447 Q 1.000** 3.159
553 N 1.000** 3.160
558 S 0.999** 3.158
565 D 1.000** 3.160
568 D 1.000** 3.160
584 D 1.000** 3.160
588 K 1.000** 3.159
618 D 1.000** 3.160
665 I 1.000** 3.159
667 N 0.800 2.718
668 P 0.996** 3.151
687 N 0.925 2.994
690 I 1.000** 3.159
691 R 0.582 2.222
694 N 0.978* 3.111
700 A 0.989* 3.135
714 Q 0.999** 3.156
732 A 1.000** 3.159
776 I 1.000** 3.159
777 C 1.000** 3.160
781 L 1.000** 3.160
791 F 0.614 2.296
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.CAP327.2.00_C6.37.KF114885_)
Pr(w>1) post mean +- SE for w
7 L 0.999** 3.498 +- 0.070
10 W 1.000** 3.500 +- 0.001
12 Q 0.962* 3.404 +- 0.487
76 V 1.000** 3.500 +- 0.010
122 T 1.000** 3.499 +- 0.039
124 A 1.000** 3.500 +- 0.000
125 N 1.000** 3.500 +- 0.000
126 L 1.000** 3.500 +- 0.000
127 K 1.000** 3.500 +- 0.000
128 E 0.998** 3.494 +- 0.120
141 Q 1.000** 3.500 +- 0.016
153 P 0.598 2.471 +- 1.255
155 N 0.990** 3.475 +- 0.251
156 Y 1.000** 3.500 +- 0.000
157 S 1.000** 3.500 +- 0.003
158 E 1.000** 3.500 +- 0.000
177 T 0.976* 3.438 +- 0.394
208 H 0.974* 3.433 +- 0.407
245 L 0.805 3.000 +- 1.016
249 A 0.934 3.331 +- 0.635
259 S 0.842 3.094 +- 0.936
261 E 0.853 3.124 +- 0.905
268 D 1.000** 3.500 +- 0.007
286 N 0.997** 3.492 +- 0.141
300 K 0.987* 3.466 +- 0.292
301 G 1.000** 3.500 +- 0.000
305 T 0.907 3.263 +- 0.742
308 K 1.000** 3.500 +- 0.033
309 R 1.000** 3.499 +- 0.053
311 E 0.916 3.284 +- 0.711
312 K 1.000** 3.500 +- 0.010
315 K 0.994** 3.484 +- 0.198
322 N 1.000** 3.500 +- 0.002
324 A 1.000** 3.500 +- 0.007
325 P 1.000** 3.500 +- 0.005
326 P 1.000** 3.499 +- 0.052
351 E 1.000** 3.500 +- 0.002
356 S 1.000** 3.500 +- 0.000
357 E 1.000** 3.500 +- 0.000
358 L 1.000** 3.500 +- 0.000
360 K 1.000** 3.500 +- 0.000
361 T 0.998** 3.494 +- 0.123
377 E 0.917 3.288 +- 0.704
388 A 1.000** 3.499 +- 0.042
394 V 1.000** 3.500 +- 0.005
408 N 1.000** 3.500 +- 0.000
409 N 1.000** 3.500 +- 0.000
410 N 1.000** 3.500 +- 0.000
411 N 1.000** 3.500 +- 0.000
412 N 1.000** 3.500 +- 0.004
447 Q 1.000** 3.499 +- 0.055
553 N 1.000** 3.500 +- 0.000
558 S 0.998** 3.496 +- 0.103
565 D 1.000** 3.500 +- 0.001
568 D 1.000** 3.500 +- 0.007
584 D 1.000** 3.500 +- 0.000
588 K 0.999** 3.497 +- 0.086
618 D 1.000** 3.500 +- 0.001
665 I 1.000** 3.500 +- 0.022
668 P 0.989* 3.473 +- 0.264
687 N 0.699 2.730 +- 1.174
690 I 1.000** 3.500 +- 0.026
694 N 0.903 3.251 +- 0.758
700 A 0.965* 3.411 +- 0.469
714 Q 0.997** 3.492 +- 0.145
732 A 1.000** 3.500 +- 0.023
776 I 0.999** 3.498 +- 0.071
777 C 1.000** 3.500 +- 0.001
781 L 1.000** 3.500 +- 0.006
