--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Mar 16 18:08:41 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -49062.58 -49102.16
2 -49062.60 -49097.89
--------------------------------------
TOTAL -49062.59 -49101.48
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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} 8.327723 0.062764 7.838347 8.804613 8.323195 721.09 782.54 1.000
r(A<->C){all} 0.142434 0.000028 0.132260 0.152749 0.142495 379.58 487.51 1.001
r(A<->G){all} 0.284031 0.000124 0.262610 0.305678 0.283619 280.03 282.84 1.002
r(A<->T){all} 0.059054 0.000010 0.052999 0.065212 0.059008 482.02 509.82 1.003
r(C<->G){all} 0.074755 0.000026 0.064612 0.084583 0.074759 350.18 419.03 1.000
r(C<->T){all} 0.356884 0.000145 0.331768 0.379038 0.356876 287.44 299.18 1.003
r(G<->T){all} 0.082843 0.000021 0.073204 0.091287 0.082788 479.90 502.08 1.001
pi(A){all} 0.399460 0.000049 0.386136 0.413828 0.399375 291.57 366.11 1.006
pi(C){all} 0.164734 0.000025 0.155195 0.174894 0.164822 281.30 326.58 1.002
pi(G){all} 0.227160 0.000032 0.215584 0.237721 0.227137 362.23 394.57 1.000
pi(T){all} 0.208646 0.000034 0.196991 0.219576 0.208743 285.37 297.72 1.001
alpha{1,2} 0.474740 0.000535 0.432417 0.519954 0.473873 921.21 1003.63 1.000
alpha{3} 1.069343 0.004589 0.944083 1.203141 1.066979 1073.09 1089.85 1.000
pinvar{all} 0.173860 0.000209 0.145213 0.200875 0.174249 1111.26 1177.50 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 -40099.699125
Model 2: PositiveSelection -39449.807234
Model 0: one-ratio -42578.476225
Model 3: discrete -39424.72764
Model 7: beta -39913.947239
Model 8: beta&w>1 -39331.455117
Model 0 vs 1 4957.554199999999
Model 2 vs 1 1299.7837819999986
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.US.04.USPI71101EI7y04051pcWG2B9.JN024210_)
Pr(w>1) post mean +- SE for w
51 A 0.766 2.981
74 K 1.000** 3.585
123 L 1.000** 3.585
124 E 1.000** 3.585
125 N 1.000** 3.585
126 T 1.000** 3.585
127 T 1.000** 3.585
128 N 1.000** 3.585
129 A 1.000** 3.585
130 A 1.000** 3.585
139 V 0.998** 3.580
146 M 0.996** 3.575
147 K 0.678 2.753
150 Y 0.995** 3.572
162 E 1.000** 3.585
163 D 1.000** 3.585
164 D 1.000** 3.585
174 I 0.954* 3.465
183 T 0.999** 3.582
214 R 0.814 3.104
251 K 0.982* 3.539
253 T 1.000** 3.585
265 V 0.991** 3.562
272 N 1.000** 3.585
280 H 0.995** 3.572
289 E 1.000** 3.585
296 Q 0.706 2.826
305 K 1.000** 3.584
308 E 0.976* 3.522
309 K 1.000** 3.585
311 V 1.000** 3.585
312 E 1.000** 3.585
315 R 0.998** 3.581
322 T 1.000** 3.585
324 K 0.998** 3.581
325 P 0.991** 3.561
326 S 1.000** 3.585
351 Q 1.000** 3.585
355 S 0.998** 3.579
357 D 1.000** 3.585
358 T 0.855 3.211
385 R 1.000** 3.585
387 Q 1.000** 3.585
391 S 0.765 2.978
405 V 1.000** 3.585
406 N 1.000** 3.585
407 T 1.000** 3.585
408 T 1.000** 3.585
443 K 1.000** 3.585
459 V 0.890 3.300
548 A 1.000** 3.585
553 A 1.000** 3.585
560 Q 1.000** 3.585
561 K 1.000** 3.585
562 Y 1.000** 3.585
580 D 1.000** 3.585
581 L 1.000** 3.585
584 N 1.000** 3.585
614 S 1.000** 3.585
661 L 1.000** 3.585
663 T 0.999** 3.583
686 G 1.000** 3.585
690 N 0.646 2.671
696 V 0.832 3.150
728 I 1.000** 3.585
751 L 0.700 2.808
772 V 1.000** 3.584
773 F 1.000** 3.585
779 L 0.513 2.326
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: B.US.04.USPI71101EI7y04051pcWG2B9.JN024210_)
Pr(w>1) post mean +- SE for w
51 A 0.793 2.982 +- 1.013
74 K 1.000** 3.500 +- 0.001
123 L 1.000** 3.500 +- 0.000
124 E 1.000** 3.500 +- 0.000
125 N 1.000** 3.500 +- 0.000
126 T 1.000** 3.500 +- 0.000
127 T 1.000** 3.500 +- 0.000
128 N 1.000** 3.500 +- 0.000
129 A 1.000** 3.500 +- 0.000
130 A 1.000** 3.500 +- 0.000
139 V 0.998** 3.495 +- 0.109
146 M 0.996** 3.491 +- 0.151
147 K 0.681 2.704 +- 1.165
150 Y 0.995** 3.488 +- 0.176
162 E 1.000** 3.500 +- 0.001
163 D 1.000** 3.500 +- 0.000
164 D 1.000** 3.500 +- 0.013
174 I 0.954* 3.385 +- 0.524
183 T 0.999** 3.497 +- 0.090
214 R 0.833 3.082 +- 0.933
251 K 0.983* 3.458 +- 0.322
253 T 1.000** 3.500 +- 0.006
265 V 0.992** 3.480 +- 0.224
272 N 1.000** 3.500 +- 0.000
280 H 0.995** 3.488 +- 0.173
289 E 1.000** 3.500 +- 0.000
296 Q 0.725 2.813 +- 1.116
305 K 1.000** 3.499 +- 0.038
308 E 0.977* 3.443 +- 0.373
309 K 1.000** 3.500 +- 0.000
311 V 1.000** 3.500 +- 0.009
312 E 1.000** 3.500 +- 0.005
315 R 0.999** 3.496 +- 0.096
322 T 1.000** 3.500 +- 0.000
324 K 0.998** 3.496 +- 0.098
325 P 0.991** 3.478 +- 0.235
326 S 1.000** 3.500 +- 0.011
351 Q 1.000** 3.500 +- 0.000
355 S 0.998** 3.495 +- 0.112
357 D 1.000** 3.500 +- 0.000
358 T 0.865 3.162 +- 0.854
385 R 1.000** 3.500 +- 0.022
387 Q 1.000** 3.500 +- 0.000
391 S 0.785 2.963 +- 1.027
405 V 1.000** 3.500 +- 0.000
406 N 1.000** 3.500 +- 0.001
407 T 1.000** 3.500 +- 0.001
408 T 1.000** 3.500 +- 0.000
443 K 1.000** 3.500 +- 0.001
459 V 0.896 3.239 +- 0.764
548 A 1.000** 3.500 +- 0.011
553 A 1.000** 3.500 +- 0.019
560 Q 1.000** 3.500 +- 0.000
561 K 1.000** 3.500 +- 0.001
562 Y 1.000** 3.500 +- 0.013
580 D 1.000** 3.500 +- 0.000
581 L 1.000** 3.500 +- 0.013
584 N 1.000** 3.500 +- 0.000
614 S 1.000** 3.500 +- 0.013
661 L 1.000** 3.500 +- 0.010
663 T 0.999** 3.498 +- 0.067
686 G 1.000** 3.500 +- 0.024
690 N 0.681 2.703 +- 1.165
696 V 0.838 3.094 +- 0.922
728 I 1.000** 3.500 +- 0.002
751 L 0.714 2.785 +- 1.130
772 V 1.000** 3.499 +- 0.041
773 F 1.000** 3.500 +- 0.009
779 L 0.537 2.341 +- 1.247
Model 8 vs 7 1164.9842440000066
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: B.US.04.USPI71101EI7y04051pcWG2B9.JN024210_)
Pr(w>1) post mean +- SE for w
51 A 0.773 2.616
74 K 1.000** 3.103
123 L 1.000** 3.103
124 E 1.000** 3.103
125 N 1.000** 3.103
126 T 1.000** 3.103
127 T 1.000** 3.103
128 N 1.000** 3.103
129 A 1.000** 3.103
130 A 1.000** 3.103
139 V 0.997** 3.098
146 M 0.994** 3.091
147 K 0.713 2.482
150 Y 0.994** 3.092
162 E 1.000** 3.103
163 D 1.000** 3.103
164 D 1.000** 3.103
174 I 0.962* 3.021
183 T 0.999** 3.101
214 R 0.807 2.689
251 K 0.979* 3.059
253 T 1.000** 3.103
265 V 0.989* 3.079
272 N 1.000** 3.103
280 H 0.994** 3.091
289 E 1.000** 3.103
296 Q 0.735 2.529
305 K 1.000** 3.103
308 E 0.970* 3.040
309 K 1.000** 3.103
311 V 1.000** 3.103
312 E 1.000** 3.103
315 R 0.998** 3.098
322 T 1.000** 3.103
324 K 0.997** 3.098
325 P 0.989* 3.081
326 S 1.000** 3.103
351 Q 1.000** 3.103
355 S 0.996** 3.096
357 D 1.000** 3.103
358 T 0.876 2.837
385 R 1.000** 3.103
387 Q 1.000** 3.103
391 S 0.785 2.640
405 V 1.000** 3.103
406 N 1.000** 3.103
407 T 1.000** 3.103
408 T 1.000** 3.103
443 K 1.000** 3.103
459 V 0.897 2.882
548 A 1.000** 3.103
553 A 1.000** 3.103
560 Q 1.000** 3.103
561 K 1.000** 3.103
562 Y 1.000** 3.103
580 D 1.000** 3.103
581 L 1.000** 3.103
584 N 1.000** 3.103
614 S 1.000** 3.103
661 L 1.000** 3.103
663 T 0.999** 3.102
686 G 1.000** 3.103
690 N 0.669 2.390
696 V 0.869 2.820
728 I 1.000** 3.103
751 L 0.749 2.561
772 V 1.000** 3.103
773 F 1.000** 3.103
779 L 0.556 2.140
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: B.US.04.USPI71101EI7y04051pcWG2B9.JN024210_)
Pr(w>1) post mean +- SE for w
74 K 1.000** 3.499 +- 0.032
123 L 1.000** 3.499 +- 0.032
124 E 1.000** 3.499 +- 0.032
125 N 1.000** 3.499 +- 0.032
126 T 1.000** 3.499 +- 0.032
127 T 1.000** 3.499 +- 0.032
128 N 1.000** 3.499 +- 0.032
129 A 1.000** 3.499 +- 0.032
130 A 1.000** 3.499 +- 0.032
139 V 0.987* 3.466 +- 0.288
146 M 0.974* 3.433 +- 0.406
150 Y 0.977* 3.441 +- 0.382
162 E 1.000** 3.499 +- 0.033
163 D 1.000** 3.499 +- 0.032
164 D 1.000** 3.498 +- 0.048
174 I 0.860 3.140 +- 0.892
183 T 0.997** 3.491 +- 0.150
251 K 0.899 3.239 +- 0.774
253 T 1.000** 3.499 +- 0.034
265 V 0.936 3.334 +- 0.629
272 N 1.000** 3.499 +- 0.032
280 H 0.974* 3.433 +- 0.406
289 E 1.000** 3.499 +- 0.032
305 K 0.998** 3.495 +- 0.105
308 E 0.852 3.119 +- 0.911
309 K 1.000** 3.499 +- 0.032
311 V 1.000** 3.499 +- 0.037
312 E 1.000** 3.499 +- 0.035
315 R 0.989* 3.471 +- 0.269
322 T 1.000** 3.499 +- 0.032
324 K 0.989* 3.471 +- 0.269
325 P 0.949 3.367 +- 0.567
326 S 1.000** 3.499 +- 0.035
351 Q 1.000** 3.499 +- 0.032
355 S 0.982* 3.454 +- 0.338
357 D 1.000** 3.499 +- 0.032
358 T 0.549 2.341 +- 1.278
385 R 0.999** 3.497 +- 0.070
387 Q 1.000** 3.499 +- 0.032
405 V 1.000** 3.499 +- 0.032
406 N 1.000** 3.499 +- 0.032
407 T 1.000** 3.499 +- 0.033
408 T 1.000** 3.499 +- 0.032
443 K 1.000** 3.499 +- 0.032
459 V 0.616 2.512 +- 1.251
548 A 1.000** 3.499 +- 0.039
553 A 1.000** 3.499 +- 0.046
560 Q 1.000** 3.499 +- 0.032
561 K 1.000** 3.499 +- 0.032
562 Y 1.000** 3.499 +- 0.046
580 D 1.000** 3.499 +- 0.032
581 L 1.000** 3.499 +- 0.042
584 N 1.000** 3.499 +- 0.032
614 S 1.000** 3.499 +- 0.042
661 L 1.000** 3.499 +- 0.036
663 T 0.997** 3.492 +- 0.133
686 G 1.000** 3.498 +- 0.063
696 V 0.575 2.403 +- 1.274
728 I 1.000** 3.499 +- 0.033
772 V 0.999** 3.496 +- 0.096
773 F 1.000** 3.499 +- 0.036
