--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Jan 28 15:22:51 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/GAG_1_4/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -18563.06 -18609.94
2 -18560.26 -18609.34
--------------------------------------
TOTAL -18560.90 -18609.68
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/HIV1_N1/GAG_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_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/GAG_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} 4.047602 0.021180 3.749631 4.316541 4.044593 1167.01 1237.70 1.000
r(A<->C){all} 0.087265 0.000031 0.076137 0.097434 0.086955 496.04 647.34 1.001
r(A<->G){all} 0.288364 0.000218 0.259681 0.317692 0.288284 449.92 476.72 1.002
r(A<->T){all} 0.049655 0.000018 0.041478 0.058003 0.049512 820.79 867.19 1.000
r(C<->G){all} 0.049329 0.000028 0.039305 0.059497 0.049335 782.67 812.62 1.000
r(C<->T){all} 0.463656 0.000303 0.426399 0.494098 0.464161 399.58 438.34 1.003
r(G<->T){all} 0.061732 0.000037 0.050452 0.073845 0.061484 736.06 775.27 1.005
pi(A){all} 0.410053 0.000087 0.393082 0.429530 0.410030 807.71 820.71 1.000
pi(C){all} 0.194451 0.000064 0.179174 0.210071 0.194309 580.42 597.49 1.001
pi(G){all} 0.221123 0.000061 0.205993 0.236699 0.221005 611.18 694.84 1.002
pi(T){all} 0.174373 0.000053 0.160729 0.189275 0.174110 612.85 689.82 1.000
alpha{1,2} 0.336032 0.000478 0.295830 0.380006 0.335225 914.10 1127.34 1.000
alpha{3} 2.013847 0.055361 1.605846 2.513976 1.998117 976.26 1191.06 1.000
pinvar{all} 0.196280 0.000494 0.153741 0.239883 0.196791 846.07 955.12 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 -16074.737989
Model 2: PositiveSelection -15994.902025
Model 0: one-ratio -17007.678345
Model 3: discrete -15927.984812
Model 7: beta -15982.055321
Model 8: beta&w>1 -15908.915041
Model 0 vs 1 1865.880712000002
Model 2 vs 1 159.67192799999975
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: A1.KE.94.clone_904.GQ430768_)
Pr(w>1) post mean +- SE for w
28 Q 1.000** 3.029
69 G 0.975* 2.978
79 F 1.000** 3.029
84 T 1.000** 3.029
91 R 0.999** 3.027
93 E 0.916 2.858
137 S 0.999** 3.027
206 T 0.804 2.631
214 I 0.999** 3.028
243 S 1.000** 3.029
271 V 0.917 2.861
294 T 0.937 2.901
323 S 0.995** 3.020
348 G 0.999** 3.027
361 V 0.671 2.361
363 Q 1.000** 3.029
449 Q 0.998** 3.026
454 V 0.999** 3.028
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: A1.KE.94.clone_904.GQ430768_)
Pr(w>1) post mean +- SE for w
28 Q 1.000** 3.416 +- 0.278
69 G 0.962* 3.324 +- 0.535
79 F 1.000** 3.416 +- 0.279
84 T 1.000** 3.416 +- 0.278
91 R 0.998** 3.412 +- 0.294
93 E 0.794 2.904 +- 1.007
137 S 0.999** 3.413 +- 0.290
206 T 0.680 2.630 +- 1.146
214 I 0.999** 3.414 +- 0.285
243 S 1.000** 3.415 +- 0.282
271 V 0.857 3.064 +- 0.885
294 T 0.879 3.118 +- 0.831
323 S 0.994** 3.403 +- 0.330
348 G 0.999** 3.413 +- 0.290
363 Q 1.000** 3.416 +- 0.277
449 Q 0.998** 3.412 +- 0.296
454 V 0.999** 3.415 +- 0.284
Model 8 vs 7 146.28055999999924
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: A1.KE.94.clone_904.GQ430768_)
Pr(w>1) post mean +- SE for w
28 Q 1.000** 2.448
69 G 0.983* 2.421
79 F 1.000** 2.448
84 T 1.000** 2.448
91 R 0.999** 2.446
93 E 0.951* 2.370
137 S 0.999** 2.447
206 T 0.876 2.251
210 Q 0.554 1.742
214 I 0.999** 2.447
243 S 1.000** 2.447
271 V 0.958* 2.382
294 T 0.968* 2.398
323 S 0.997** 2.443
348 G 0.999** 2.447
361 V 0.821 2.167
363 Q 1.000** 2.448
449 Q 0.999** 2.446
454 V 1.000** 2.447
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: A1.KE.94.clone_904.GQ430768_)
Pr(w>1) post mean +- SE for w
28 Q 1.000** 2.500 +- 0.018
69 G 0.979* 2.468 +- 0.224
79 F 1.000** 2.500 +- 0.023
84 T 1.000** 2.500 +- 0.016
91 R 0.998** 2.497 +- 0.064
93 E 0.932 2.393 +- 0.396
137 S 0.999** 2.498 +- 0.052
206 T 0.860 2.278 +- 0.551
210 Q 0.516 1.731 +- 0.796
214 I 0.999** 2.499 +- 0.043
243 S 1.000** 2.499 +- 0.034
271 V 0.950* 2.422 +- 0.343
294 T 0.960* 2.437 +- 0.308
323 S 0.996** 2.494 +- 0.097
348 G 0.999** 2.498 +- 0.050
361 V 0.743 2.097 +- 0.686
363 Q 1.000** 2.500 +- 0.003
449 Q 0.998** 2.497 +- 0.065
454 V 0.999** 2.499 +- 0.036
