--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Jan 26 01:38:09 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -47574.84 -47619.35
2 -47575.23 -47618.20
--------------------------------------
TOTAL -47575.02 -47618.93
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/ENV_1_4/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_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 7.748828 0.046437 7.351036 8.165507 7.745057 1022.37 1037.23 1.000
r(A<->C){all} 0.130021 0.000025 0.120680 0.139947 0.129875 429.33 460.64 1.002
r(A<->G){all} 0.302603 0.000117 0.280696 0.322816 0.302699 235.43 263.58 1.014
r(A<->T){all} 0.060401 0.000010 0.054216 0.066392 0.060381 506.54 673.28 1.000
r(C<->G){all} 0.069583 0.000025 0.059879 0.079438 0.069256 434.43 473.34 1.002
r(C<->T){all} 0.339722 0.000133 0.318179 0.362378 0.339234 247.05 307.01 1.017
r(G<->T){all} 0.097670 0.000023 0.088453 0.107563 0.097525 287.68 470.99 1.003
pi(A){all} 0.387628 0.000047 0.374024 0.400839 0.387767 454.91 455.51 1.000
pi(C){all} 0.182606 0.000024 0.172544 0.191875 0.182592 342.98 402.93 1.008
pi(G){all} 0.213580 0.000029 0.202984 0.224087 0.213451 356.18 377.00 1.017
pi(T){all} 0.216186 0.000035 0.205095 0.228336 0.216252 371.90 396.89 1.005
alpha{1,2} 0.467455 0.000489 0.426679 0.511776 0.466613 1148.31 1172.51 1.000
alpha{3} 1.074649 0.005165 0.944838 1.223442 1.070980 1013.18 1226.76 1.000
pinvar{all} 0.175622 0.000208 0.147828 0.202891 0.175615 1041.35 1121.90 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 -37442.164166
Model 2: PositiveSelection -36887.367584
Model 0: one-ratio -39726.536894
Model 3: discrete -36879.498558
Model 7: beta -37287.202195
Model 8: beta&w>1 -36784.671892
Model 0 vs 1 4568.74545599999
Model 2 vs 1 1109.5931640000053
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 02_AG.US.01.APV_12.DQ869018_)
Pr(w>1) post mean +- SE for w
7 Y 1.000** 3.581
9 C 0.852 3.201
12 I 0.883 3.281
74 H 1.000** 3.582
120 Q 1.000** 3.582
121 D 0.985* 3.543
122 F 1.000** 3.582
123 M 1.000** 3.582
132 I 0.998** 3.577
140 R 1.000** 3.582
154 D 0.673 2.738
155 S 1.000** 3.582
165 A 0.846 3.184
247 T 0.555 2.432
257 K 0.997** 3.574
264 G 0.968* 3.499
272 R 1.000** 3.582
283 D 1.000** 3.582
297 K 0.764 2.971
298 A 1.000** 3.582
299 Q 1.000** 3.582
302 K 1.000** 3.582
305 Q 1.000** 3.582
306 E 1.000** 3.582
308 A 1.000** 3.582
309 K 1.000** 3.582
319 N 1.000** 3.582
321 N 1.000** 3.582
322 K 1.000** 3.581
348 A 1.000** 3.582
352 T 1.000** 3.582
353 I 1.000** 3.582
355 D 1.000** 3.582
382 A 1.000** 3.582
384 E 1.000** 3.582
388 E 0.987* 3.548
402 N 1.000** 3.582
403 S 0.785 3.027
438 R 0.787 3.033
543 D 0.728 2.881
548 S 0.998** 3.576
554 Y 1.000** 3.582
555 N 1.000** 3.582
556 D 0.617 2.592
572 S 1.000** 3.582
601 S 1.000** 3.582
647 P 0.841 3.171
648 T 1.000** 3.581
650 H 1.000** 3.581
651 Q 0.999** 3.580
673 V 1.000** 3.582
683 A 1.000** 3.582
697 R 0.703 2.814
711 A 0.979* 3.526
720 S 0.839 3.166
747 I 0.726 2.875
751 T 0.999** 3.580
752 G 0.965* 3.492
756 R 0.996** 3.571
766 L 0.998** 3.575
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: 02_AG.US.01.APV_12.DQ869018_)
Pr(w>1) post mean +- SE for w
7 Y 1.000** 3.500 +- 0.027
9 C 0.877 3.191 +- 0.822
12 I 0.901 3.254 +- 0.745
74 H 1.000** 3.500 +- 0.001
120 Q 1.000** 3.500 +- 0.000
121 D 0.988* 3.471 +- 0.267
122 F 1.000** 3.500 +- 0.000
123 M 1.000** 3.500 +- 0.000
132 I 0.999** 3.496 +- 0.095
140 R 1.000** 3.500 +- 0.017
154 D 0.740 2.849 +- 1.097
155 S 1.000** 3.500 +- 0.000
165 A 0.866 3.165 +- 0.852
247 T 0.616 2.539 +- 1.216
257 K 0.997** 3.494 +- 0.127
264 G 0.974* 3.434 +- 0.400
272 R 1.000** 3.500 +- 0.002
283 D 1.000** 3.500 +- 0.002
297 K 0.814 3.034 +- 0.974
298 A 1.000** 3.500 +- 0.000
299 Q 1.000** 3.500 +- 0.000
302 K 1.000** 3.500 +- 0.001
305 Q 1.000** 3.500 +- 0.001
306 E 1.000** 3.500 +- 0.005
308 A 1.000** 3.500 +- 0.000
309 K 1.000** 3.500 +- 0.002
319 N 1.000** 3.500 +- 0.001
321 N 1.000** 3.500 +- 0.019
322 K 1.000** 3.499 +- 0.049
348 A 1.000** 3.500 +- 0.000
352 T 1.000** 3.500 +- 0.000
353 I 1.000** 3.500 +- 0.000
355 D 1.000** 3.500 +- 0.000
382 A 1.000** 3.500 +- 0.002
384 E 1.000** 3.500 +- 0.000
388 E 0.989* 3.473 +- 0.258
402 N 1.000** 3.500 +- 0.000
403 S 0.822 3.056 +- 0.956
438 R 0.826 3.066 +- 0.947
543 D 0.769 2.923 +- 1.053
548 S 0.998** 3.495 +- 0.111
554 Y 1.000** 3.500 +- 0.000
555 N 1.000** 3.500 +- 0.000
556 D 0.679 2.698 +- 1.167
572 S 1.000** 3.500 +- 0.000
601 S 1.000** 3.500 +- 0.002
647 P 0.862 3.156 +- 0.861
648 T 1.000** 3.500 +- 0.035
650 H 1.000** 3.499 +- 0.052
651 Q 0.999** 3.499 +- 0.056
673 V 1.000** 3.500 +- 0.002
683 A 1.000** 3.500 +- 0.004
697 R 0.734 2.834 +- 1.105
711 A 0.981* 3.453 +- 0.339
720 S 0.857 3.143 +- 0.875
747 I 0.781 2.952 +- 1.034
751 T 0.999** 3.498 +- 0.061
752 G 0.970* 3.425 +- 0.426
756 R 0.996** 3.491 +- 0.154
766 L 0.998** 3.494 +- 0.118
Model 8 vs 7 1005.0606059999991
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 02_AG.US.01.APV_12.DQ869018_)
Pr(w>1) post mean +- SE for w
7 Y 1.000** 3.160
9 C 0.865 2.862
12 I 0.899 2.936
74 H 1.000** 3.160
120 Q 1.000** 3.160
121 D 0.982* 3.121
122 F 1.000** 3.160
123 M 1.000** 3.160
132 I 0.998** 3.155
140 R 1.000** 3.160
154 D 0.674 2.444
155 S 1.000** 3.160
165 A 0.877 2.888
247 T 0.633 2.349
257 K 0.996** 3.150
264 G 0.968* 3.089
272 R 1.000** 3.160
283 D 1.000** 3.160
297 K 0.783 2.683
298 A 1.000** 3.160
299 Q 1.000** 3.160
302 K 1.000** 3.160
305 Q 1.000** 3.160
306 E 1.000** 3.160
308 A 1.000** 3.160
309 K 1.000** 3.160
319 N 1.000** 3.160
321 N 1.000** 3.160
322 K 0.999** 3.159
348 A 1.000** 3.160
352 T 1.000** 3.160
353 I 1.000** 3.160
355 D 1.000** 3.160
382 A 1.000** 3.160
384 E 1.000** 3.160
388 E 0.986* 3.129
402 N 1.000** 3.160
403 S 0.795 2.707
438 R 0.810 2.742
543 D 0.773 2.658
548 S 0.998** 3.155
554 Y 1.000** 3.160
555 N 1.000** 3.160
556 D 0.648 2.385
572 S 1.000** 3.160
601 S 1.000** 3.160
647 P 0.871 2.874
648 T 1.000** 3.159
650 H 0.999** 3.159
651 Q 0.999** 3.159
673 V 1.000** 3.160
683 A 1.000** 3.160
697 R 0.756 2.617
711 A 0.982* 3.120
720 S 0.851 2.829
747 I 0.753 2.617
751 T 0.999** 3.158
752 G 0.968* 3.089
756 R 0.996** 3.151
766 L 0.997** 3.153
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: 02_AG.US.01.APV_12.DQ869018_)
Pr(w>1) post mean +- SE for w
7 Y 1.000** 3.499 +- 0.042
9 C 0.618 2.519 +- 1.249
12 I 0.713 2.761 +- 1.164
74 H 1.000** 3.500 +- 0.001
120 Q 1.000** 3.500 +- 0.001
121 D 0.924 3.306 +- 0.677
122 F 1.000** 3.500 +- 0.001
123 M 1.000** 3.500 +- 0.001
132 I 0.993** 3.483 +- 0.210
140 R 1.000** 3.500 +- 0.033
155 S 1.000** 3.500 +- 0.001
165 A 0.689 2.700 +- 1.192
257 K 0.985* 3.463 +- 0.306
264 G 0.891 3.220 +- 0.800
272 R 1.000** 3.500 +- 0.003
283 D 1.000** 3.500 +- 0.004
298 A 1.000** 3.500 +- 0.001
299 Q 1.000** 3.500 +- 0.001
302 K 1.000** 3.500 +- 0.002
305 Q 1.000** 3.500 +- 0.002
306 E 1.000** 3.500 +- 0.008
308 A 1.000** 3.500 +- 0.001
309 K 1.000** 3.500 +- 0.003
319 N 1.000** 3.500 +- 0.002
321 N 1.000** 3.499 +- 0.039
322 K 0.998** 3.496 +- 0.102
348 A 1.000** 3.500 +- 0.001
352 T 1.000** 3.500 +- 0.001
353 I 1.000** 3.500 +- 0.001
355 D 1.000** 3.500 +- 0.001
382 A 1.000** 3.500 +- 0.004
384 E 1.000** 3.500 +- 0.001
388 E 0.953* 3.379 +- 0.544
402 N 1.000** 3.500 +- 0.001
548 S 0.995** 3.488 +- 0.178
554 Y 1.000** 3.500 +- 0.001
555 N 1.000** 3.500 +- 0.001
572 S 1.000** 3.500 +- 0.001
601 S 1.000** 3.500 +- 0.004
647 P 0.668 2.645 +- 1.213
648 T 1.000** 3.499 +- 0.049
650 H 0.999** 3.497 +- 0.088
651 Q 0.999** 3.497 +- 0.084
673 V 1.000** 3.500 +- 0.004
683 A 1.000** 3.500 +- 0.005
711 A 0.953* 3.378 +- 0.546
720 S 0.654 2.608 +- 1.227
751 T 0.998** 3.495 +- 0.114
752 G 0.908 3.265 +- 0.741
756 R 0.992** 3.481 +- 0.223
766 L 0.993** 3.481 +- 0.218
