--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Mar 17 15:12:37 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_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -49724.95 -49772.04
2 -49725.94 -49766.57
--------------------------------------
TOTAL -49725.33 -49771.35
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/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_A1/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} 8.462852 0.048676 8.059313 8.913363 8.458578 1088.13 1190.79 1.001
r(A<->C){all} 0.134779 0.000025 0.124888 0.144370 0.134708 381.13 420.20 1.002
r(A<->G){all} 0.298388 0.000096 0.279658 0.317868 0.298196 299.48 328.54 1.002
r(A<->T){all} 0.054721 0.000009 0.049071 0.060394 0.054632 506.28 537.13 1.000
r(C<->G){all} 0.079657 0.000026 0.070332 0.089950 0.079573 557.67 614.70 1.000
r(C<->T){all} 0.340936 0.000111 0.320068 0.360484 0.340866 319.88 328.08 1.003
r(G<->T){all} 0.091518 0.000022 0.082686 0.100737 0.091465 458.48 486.47 1.001
pi(A){all} 0.397717 0.000044 0.384921 0.410402 0.397990 423.01 437.26 1.000
pi(C){all} 0.173452 0.000023 0.164095 0.182634 0.173347 283.01 364.68 1.004
pi(G){all} 0.213848 0.000023 0.203784 0.222593 0.213859 636.69 639.63 1.007
pi(T){all} 0.214983 0.000032 0.203765 0.225667 0.214934 394.62 416.75 1.000
alpha{1,2} 0.483987 0.000525 0.440416 0.528128 0.482779 1041.00 1054.31 1.002
alpha{3} 1.058125 0.003776 0.945884 1.184467 1.058257 1163.56 1241.72 1.000
pinvar{all} 0.168000 0.000184 0.142712 0.196071 0.167635 978.20 1109.43 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 -41777.178034
Model 2: PositiveSelection -41031.166056
Model 0: one-ratio -44475.690467
Model 3: discrete -40991.78024
Model 7: beta -41552.440307
Model 8: beta&w>1 -40894.759678
Model 0 vs 1 5397.024866000007
Model 2 vs 1 1492.02395599999
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.10.DEMB10US011.KC473830_)
Pr(w>1) post mean +- SE for w
8 C 0.967* 3.631
69 E 1.000** 3.720
115 E 1.000** 3.720
116 T 1.000** 3.720
117 N 1.000** 3.720
118 T 1.000** 3.720
119 T 1.000** 3.720
120 N 1.000** 3.720
121 A 1.000** 3.720
122 T 1.000** 3.720
123 A 1.000** 3.720
134 D 0.984* 3.678
150 K 0.981* 3.670
153 G 0.998** 3.714
154 N 1.000** 3.720
155 T 1.000** 3.720
174 S 0.999** 3.718
205 N 0.993** 3.702
245 A 0.940 3.558
257 N 1.000** 3.720
272 H 1.000** 3.720
282 A 1.000** 3.720
296 R 1.000** 3.720
297 A 1.000** 3.720
298 Q 1.000** 3.720
301 N 1.000** 3.720
304 Q 0.999** 3.718
305 K 1.000** 3.720
307 A 1.000** 3.720
308 T 1.000** 3.719
311 G 1.000** 3.720
319 S 1.000** 3.720
321 K 1.000** 3.720
322 N 1.000** 3.720
323 S 0.999** 3.717
348 Q 1.000** 3.720
352 R 1.000** 3.720
353 S 1.000** 3.720
354 D 1.000** 3.720
381 K 0.998** 3.716
383 L 1.000** 3.720
401 N 1.000** 3.720
402 D 1.000** 3.720
403 T 1.000** 3.720
404 L 1.000** 3.720
546 N 1.000** 3.720
551 N 0.992** 3.699
557 L 1.000** 3.720
558 S 1.000** 3.720
559 D 1.000** 3.720
578 S 1.000** 3.720
579 I 1.000** 3.720
582 T 1.000** 3.720
589 N 0.981* 3.668
612 D 1.000** 3.720
659 L 1.000** 3.720
661 A 1.000** 3.720
662 P 1.000** 3.720
684 E 1.000** 3.720
688 D 0.995** 3.707
694 F 1.000** 3.720
718 R 0.998** 3.714
723 L 0.784 3.133
763 L 0.778 3.116
764 V 1.000** 3.720
767 I 1.000** 3.720
768 C 1.000** 3.720
772 C 1.000** 3.720
782 A 1.000** 3.720
787 V 0.559 2.522
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.10.DEMB10US011.KC473830_)
Pr(w>1) post mean +- SE for w
8 C 0.973* 3.432 +- 0.408
69 E 1.000** 3.500 +- 0.007
115 E 1.000** 3.500 +- 0.000
116 T 1.000** 3.500 +- 0.000
117 N 1.000** 3.500 +- 0.001
118 T 1.000** 3.500 +- 0.000
119 T 1.000** 3.500 +- 0.000
120 N 1.000** 3.500 +- 0.000
121 A 1.000** 3.500 +- 0.000
122 T 1.000** 3.500 +- 0.000
123 A 1.000** 3.500 +- 0.000
134 D 0.988* 3.471 +- 0.269
150 K 0.986* 3.466 +- 0.290
153 G 0.998** 3.496 +- 0.102
154 N 1.000** 3.500 +- 0.001
155 T 1.000** 3.500 +- 0.002
165 V 0.503 2.258 +- 1.250
174 S 0.999** 3.497 +- 0.080
197 T 0.519 2.298 +- 1.249
205 N 0.995** 3.487 +- 0.178
245 A 0.956* 3.390 +- 0.512
257 N 1.000** 3.500 +- 0.017
264 N 0.536 2.340 +- 1.247
272 H 1.000** 3.500 +- 0.007
282 A 1.000** 3.500 +- 0.007
296 R 1.000** 3.500 +- 0.001
297 A 1.000** 3.500 +- 0.000
298 Q 1.000** 3.500 +- 0.002
301 N 1.000** 3.500 +- 0.004
304 Q 0.999** 3.498 +- 0.065
305 K 1.000** 3.500 +- 0.001
307 A 1.000** 3.500 +- 0.001
308 T 1.000** 3.499 +- 0.037
311 G 1.000** 3.500 +- 0.013
319 S 1.000** 3.500 +- 0.000
321 K 1.000** 3.500 +- 0.003
322 N 1.000** 3.500 +- 0.025
323 S 0.999** 3.497 +- 0.092
348 Q 1.000** 3.500 +- 0.003
352 R 1.000** 3.500 +- 0.003
353 S 1.000** 3.500 +- 0.000
354 D 1.000** 3.500 +- 0.000
381 K 0.999** 3.497 +- 0.085
383 L 1.000** 3.500 +- 0.002
401 N 1.000** 3.500 +- 0.001
402 D 1.000** 3.500 +- 0.000
403 T 1.000** 3.500 +- 0.000
404 L 1.000** 3.500 +- 0.002
546 N 1.000** 3.500 +- 0.001
551 N 0.993** 3.483 +- 0.204
557 L 1.000** 3.500 +- 0.000
558 S 1.000** 3.500 +- 0.003
559 D 1.000** 3.500 +- 0.000
578 S 1.000** 3.500 +- 0.000
579 I 1.000** 3.500 +- 0.004
582 T 1.000** 3.500 +- 0.007
589 N 0.986* 3.466 +- 0.291
612 D 1.000** 3.500 +- 0.001
659 L 1.000** 3.500 +- 0.016
661 A 1.000** 3.500 +- 0.020
662 P 1.000** 3.500 +- 0.007
684 E 1.000** 3.500 +- 0.002
688 D 0.997** 3.492 +- 0.145
694 F 1.000** 3.500 +- 0.004
718 R 0.997** 3.494 +- 0.126
723 L 0.831 3.078 +- 0.937
763 L 0.848 3.121 +- 0.897
764 V 1.000** 3.500 +- 0.018
767 I 1.000** 3.500 +- 0.008
768 C 1.000** 3.500 +- 0.008
772 C 1.000** 3.500 +- 0.011
782 A 1.000** 3.500 +- 0.001
787 V 0.657 2.641 +- 1.187
Model 8 vs 7 1315.36125799999
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.10.DEMB10US011.KC473830_)
Pr(w>1) post mean +- SE for w
8 C 0.967* 3.144
69 E 1.000** 3.219
115 E 1.000** 3.219
116 T 1.000** 3.219
117 N 1.000** 3.219
118 T 1.000** 3.219
119 T 1.000** 3.219
120 N 1.000** 3.219
121 A 1.000** 3.219
122 T 1.000** 3.219
123 A 1.000** 3.219
134 D 0.978* 3.170
150 K 0.978* 3.169
153 G 0.995** 3.209
154 N 1.000** 3.219
155 T 1.000** 3.219
174 S 0.999** 3.217
205 N 0.991** 3.198
245 A 0.946 3.098
257 N 1.000** 3.219
272 H 1.000** 3.219
282 A 1.000** 3.219
296 R 1.000** 3.219
297 A 1.000** 3.219
298 Q 1.000** 3.219
301 N 1.000** 3.219
304 Q 0.998** 3.216
305 K 1.000** 3.219
307 A 1.000** 3.219
308 T 1.000** 3.218
311 G 1.000** 3.219
319 S 1.000** 3.219
321 K 1.000** 3.219
322 N 1.000** 3.219
323 S 0.999** 3.216
348 Q 1.000** 3.219
352 R 1.000** 3.219
353 S 1.000** 3.219
354 D 1.000** 3.219
381 K 0.997** 3.213
383 L 1.000** 3.219
401 N 1.000** 3.219
402 D 1.000** 3.219
403 T 1.000** 3.219
404 L 1.000** 3.219
546 N 1.000** 3.219
551 N 0.991** 3.199
557 L 1.000** 3.219
558 S 1.000** 3.219
559 D 1.000** 3.219
578 S 1.000** 3.219
579 I 1.000** 3.219
582 T 1.000** 3.219
589 N 0.975* 3.163
612 D 1.000** 3.219
659 L 1.000** 3.219
661 A 1.000** 3.219
662 P 1.000** 3.219
684 E 1.000** 3.219
688 D 0.993** 3.203
694 F 1.000** 3.219
718 R 0.997** 3.213
723 L 0.827 2.826
763 L 0.756 2.667
764 V 1.000** 3.219
767 I 1.000** 3.219
768 C 1.000** 3.219
772 C 1.000** 3.219
782 A 1.000** 3.219
787 V 0.563 2.225
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.10.DEMB10US011.KC473830_)
Pr(w>1) post mean +- SE for w
8 C 0.909 3.266 +- 0.740
69 E 1.000** 3.500 +- 0.013
115 E 1.000** 3.500 +- 0.001
116 T 1.000** 3.500 +- 0.001
117 N 1.000** 3.500 +- 0.001
118 T 1.000** 3.500 +- 0.001
119 T 1.000** 3.500 +- 0.001
120 N 1.000** 3.500 +- 0.001
121 A 1.000** 3.500 +- 0.001
122 T 1.000** 3.500 +- 0.001
123 A 1.000** 3.500 +- 0.001
134 D 0.934 3.331 +- 0.636
150 K 0.928 3.316 +- 0.662
153 G 0.986* 3.465 +- 0.298
154 N 1.000** 3.500 +- 0.002
155 T 1.000** 3.500 +- 0.005
174 S 0.998** 3.495 +- 0.114
205 N 0.973* 3.430 +- 0.418
245 A 0.838 3.084 +- 0.946
257 N 1.000** 3.499 +- 0.044
272 H 1.000** 3.500 +- 0.014
282 A 1.000** 3.500 +- 0.015
296 R 1.000** 3.500 +- 0.002
297 A 1.000** 3.500 +- 0.001
298 Q 1.000** 3.500 +- 0.005
301 N 1.000** 3.500 +- 0.009
304 Q 0.996** 3.490 +- 0.162
305 K 1.000** 3.500 +- 0.001
307 A 1.000** 3.500 +- 0.001
308 T 0.999** 3.498 +- 0.080
311 G 1.000** 3.500 +- 0.033
319 S 1.000** 3.500 +- 0.001
321 K 1.000** 3.500 +- 0.008
322 N 0.999** 3.499 +- 0.059
323 S 0.997** 3.493 +- 0.131
348 Q 1.000** 3.500 +- 0.007
352 R 1.000** 3.500 +- 0.009
353 S 1.000** 3.500 +- 0.001
354 D 1.000** 3.500 +- 0.001
381 K 0.991** 3.477 +- 0.241
383 L 1.000** 3.500 +- 0.003
401 N 1.000** 3.500 +- 0.003
402 D 1.000** 3.500 +- 0.001
403 T 1.000** 3.500 +- 0.001
404 L 1.000** 3.500 +- 0.004
546 N 1.000** 3.500 +- 0.001
551 N 0.976* 3.439 +- 0.391
557 L 1.000** 3.500 +- 0.001
558 S 1.000** 3.500 +- 0.008
559 D 1.000** 3.500 +- 0.001
578 S 1.000** 3.500 +- 0.001
579 I 1.000** 3.500 +- 0.007
582 T 1.000** 3.500 +- 0.014
589 N 0.918 3.289 +- 0.705
612 D 1.000** 3.500 +- 0.003
659 L 1.000** 3.500 +- 0.023
661 A 1.000** 3.500 +- 0.036
662 P 1.000** 3.500 +- 0.009
684 E 1.000** 3.500 +- 0.005
688 D 0.977* 3.441 +- 0.385
694 F 1.000** 3.500 +- 0.007
718 R 0.994** 3.486 +- 0.191
723 L 0.598 2.464 +- 1.264
764 V 1.000** 3.499 +- 0.040
767 I 1.000** 3.500 +- 0.013
768 C 1.000** 3.500 +- 0.014
772 C 1.000** 3.500 +- 0.015
782 A 1.000** 3.500 +- 0.002
