--- 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