--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Jan 27 19:14:20 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_2/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -17418.94 -17467.06 2 -17416.52 -17465.71 -------------------------------------- TOTAL -17417.13 -17466.60 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/GAG_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.664582 0.017174 3.415009 3.920539 3.661478 1363.17 1390.21 1.000 r(A<->C){all} 0.085815 0.000029 0.075024 0.095867 0.085780 699.61 731.79 1.000 r(A<->G){all} 0.325048 0.000258 0.294321 0.356344 0.324665 417.94 443.89 1.001 r(A<->T){all} 0.047500 0.000017 0.039042 0.055214 0.047451 580.17 764.70 1.001 r(C<->G){all} 0.045901 0.000027 0.035866 0.055888 0.045822 569.97 690.70 1.000 r(C<->T){all} 0.429957 0.000315 0.394593 0.463562 0.430299 399.84 448.78 1.001 r(G<->T){all} 0.065779 0.000040 0.054040 0.079132 0.065706 664.68 778.67 1.001 pi(A){all} 0.414011 0.000091 0.395456 0.432463 0.413935 733.21 788.57 1.000 pi(C){all} 0.196870 0.000060 0.181473 0.211808 0.196789 647.45 727.51 1.003 pi(G){all} 0.211998 0.000059 0.196424 0.225968 0.211954 397.34 552.99 1.004 pi(T){all} 0.177121 0.000053 0.163057 0.191572 0.177010 529.57 625.78 1.000 alpha{1,2} 0.316913 0.000474 0.275851 0.361655 0.316001 941.95 1078.66 1.000 alpha{3} 2.280095 0.089029 1.745101 2.915918 2.261138 1244.40 1329.12 1.000 pinvar{all} 0.177769 0.000546 0.128612 0.219657 0.177672 947.50 1073.38 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 -15746.913577 Model 2: PositiveSelection -15685.569871 Model 0: one-ratio -16603.611266 Model 3: discrete -15606.785351 Model 7: beta -15645.983528 Model 8: beta&w>1 -15582.541691 Model 0 vs 1 1713.395378000001 Model 2 vs 1 122.68741199999931 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.CM.07.BS65.JX244941_) Pr(w>1) post mean +- SE for w 13 A 0.635 2.046 26 K 0.988* 2.626 29 L 0.746 2.229 65 A 0.845 2.392 77 Y 0.999** 2.645 82 T 0.997** 2.641 88 Q 0.877 2.444 89 R 1.000** 2.647 91 E 0.763 2.256 125 T 0.829 2.366 133 P 1.000** 2.646 202 V 0.977* 2.608 210 N 0.987* 2.625 229 N 0.512 1.843 239 S 1.000** 2.647 344 S 0.913 2.503 359 Q 1.000** 2.646 360 G 0.612 2.008 434 S 0.878 2.446 454 V 0.999** 2.646 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: 01_AE.CM.07.BS65.JX244941_) Pr(w>1) post mean +- SE for w 13 A 0.651 1.977 +- 0.716 26 K 0.984* 2.485 +- 0.214 29 L 0.723 2.087 +- 0.675 65 A 0.811 2.223 +- 0.595 77 Y 0.999** 2.508 +- 0.112 82 T 0.995** 2.502 +- 0.146 88 Q 0.864 2.300 +- 0.520 89 R 1.000** 2.510 +- 0.099 91 E 0.748 2.124 +- 0.655 125 T 0.798 2.202 +- 0.610 133 P 1.000** 2.509 +- 0.103 202 V 0.968* 2.462 +- 0.282 210 N 0.981* 2.482 +- 0.225 239 S 1.000** 2.510 +- 0.100 344 S 0.893 2.347 +- 0.473 359 Q 1.000** 2.510 +- 0.101 360 G 0.590 1.887 +- 0.740 434 S 0.862 2.297 +- 0.524 454 V 0.999** 2.509 +- 0.108 Model 8 vs 7 126.88367400000061 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.CM.07.BS65.JX244941_) Pr(w>1) post mean +- SE for w 13 A 0.946 1.987 26 K 0.998** 2.051 28 K 0.796 1.800 29 L 0.937 1.975 65 A 0.964* 2.009 73 V 0.756 1.745 77 Y 1.000** 2.054 82 T 0.999** 2.053 88 Q 0.978* 2.027 89 R 1.000** 2.054 91 E 0.953* 1.996 111 D 0.656 1.622 114 H 0.820 1.829 125 T 0.961* 2.005 133 P 1.000** 2.054 134 L 0.760 1.756 202 V 0.995** 2.048 210 N 0.997** 2.051 229 N 0.848 1.864 239 S 1.000** 2.054 267 V 0.545 1.477 344 S 0.982* 2.032 359 Q 1.000** 2.054 360 G 0.901 1.930 374 I 0.757 1.750 434 S 0.978* 2.027 454 V 1.000** 2.054 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: 01_AE.CM.07.BS65.JX244941_) Pr(w>1) post mean +- SE for w 13 A 0.533 1.767 +- 0.785 26 K 0.986* 2.479 +- 0.181 29 L 0.720 2.057 +- 0.711 65 A 0.892 2.329 +- 0.492 73 V 0.523 1.729 +- 0.811 77 Y 1.000** 2.499 +- 0.032 82 T 0.998** 2.497 +- 0.073 88 Q 0.840 2.249 +- 0.576 89 R 1.000** 2.500 +- 0.001 91 E 0.730 2.074 +- 0.701 125 T 0.863 2.283 +- 0.545 133 P 1.000** 2.500 +- 0.017 202 V 0.982* 2.471 +- 0.212 210 N 0.989* 2.483 +- 0.162 229 N 0.582 1.832 +- 0.790 239 S 1.000** 2.500 +- 0.011 344 S 0.927 2.385 +- 0.410 359 Q 1.000** 2.500 +- 0.015 360 G 0.620 1.897 +- 0.771 434 S 0.872 2.298 +- 0.527 454 V 1.000** 2.499 +- 0.029