--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Feb 10 03:36:34 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_N2/POL_1_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_1/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_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -29294.16 -29335.91 2 -29290.05 -29330.12 -------------------------------------- TOTAL -29290.73 -29335.22 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_1/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_N2/POL_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.025380 0.007731 2.849271 3.191844 3.024690 1211.82 1315.97 1.000 r(A<->C){all} 0.077046 0.000016 0.069749 0.084951 0.077051 698.39 706.38 1.000 r(A<->G){all} 0.372788 0.000185 0.345021 0.398314 0.372560 332.90 383.68 1.002 r(A<->T){all} 0.038019 0.000007 0.033240 0.043029 0.037954 664.41 704.96 1.000 r(C<->G){all} 0.029808 0.000013 0.023045 0.037032 0.029563 805.87 871.35 1.000 r(C<->T){all} 0.443925 0.000205 0.414947 0.469977 0.444149 327.31 362.21 1.002 r(G<->T){all} 0.038414 0.000012 0.031867 0.045197 0.038370 799.50 808.66 1.002 pi(A){all} 0.405195 0.000052 0.390890 0.418645 0.405402 671.93 683.87 1.000 pi(C){all} 0.178187 0.000031 0.167600 0.189189 0.178153 582.61 582.62 1.000 pi(G){all} 0.206618 0.000035 0.194570 0.218007 0.206711 592.97 691.75 1.002 pi(T){all} 0.210000 0.000037 0.198688 0.222128 0.210029 556.26 583.72 1.001 alpha{1,2} 0.267008 0.000223 0.238769 0.296443 0.266618 1155.38 1297.75 1.000 alpha{3} 2.327650 0.066804 1.810664 2.801887 2.316513 975.66 1202.89 1.002 pinvar{all} 0.265641 0.000352 0.230841 0.303320 0.265794 1030.77 1154.94 1.001 ------------------------------------------------------------------------------------------------------ * 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 -28722.613283 Model 2: PositiveSelection -28636.150282 Model 0: one-ratio -30080.551681 Model 3: discrete -28515.40265 Model 7: beta -28566.048946 Model 8: beta&w>1 -28460.402236 Model 0 vs 1 2715.876796000004 Model 2 vs 1 172.92600200000015 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.TH.05.AA029b10L.JX447033_) Pr(w>1) post mean +- SE for w 16 S 0.980* 3.311 30 G 0.998** 3.354 42 F 0.899 3.120 44 F 0.669 2.578 107 L 1.000** 3.359 266 S 1.000** 3.359 350 A 0.943 3.225 354 S 0.999** 3.357 388 E 1.000** 3.359 429 A 0.988* 3.331 477 Q 1.000** 3.358 519 A 0.996** 3.349 595 L 0.958* 3.259 611 S 0.992** 3.340 626 H 1.000** 3.358 697 S 1.000** 3.359 720 S 0.504 2.189 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.TH.05.AA029b10L.JX447033_) Pr(w>1) post mean +- SE for w 16 S 0.990* 3.454 +- 0.286 30 G 0.999** 3.477 +- 0.164 41 S 0.549 2.359 +- 1.237 42 F 0.942 3.334 +- 0.598 44 F 0.790 2.957 +- 1.018 107 L 1.000** 3.479 +- 0.144 266 S 1.000** 3.479 +- 0.145 350 A 0.967* 3.398 +- 0.463 354 S 1.000** 3.478 +- 0.151 388 E 1.000** 3.479 +- 0.144 429 A 0.994** 3.464 +- 0.238 477 Q 1.000** 3.479 +- 0.148 519 A 0.998** 3.474 +- 0.184 595 L 0.977* 3.421 +- 0.401 611 S 0.996** 3.470 +- 0.210 626 H 1.000** 3.478 +- 0.149 697 S 1.000** 3.479 +- 0.144 720 S 0.607 2.499 +- 1.213 804 L 0.595 2.473 +- 1.221 Model 8 vs 7 211.2934199999945 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.TH.05.AA029b10L.JX447033_) Pr(w>1) post mean +- SE for w 11 K 0.863 2.215 16 S 0.998** 2.447 21 A 0.822 2.143 30 G 1.000** 2.450 41 S 0.834 2.161 42 F 0.993** 2.438 44 F 0.949 2.361 107 L 1.000** 2.450 266 S 1.000** 2.450 278 I 0.874 2.233 305 C 0.657 1.859 350 A 0.998** 2.446 354 S 1.000** 2.450 358 T 0.802 2.107 388 E 1.000** 2.450 429 A 0.999** 2.449 477 Q 1.000** 2.450 519 A 1.000** 2.450 595 L 0.998** 2.446 611 S 0.999** 2.449 626 H 1.000** 2.450 634 S 0.941 2.349 697 S 1.000** 2.450 720 S 0.978* 2.412 775 V 0.916 2.305 804 L 0.870 2.225 827 A 0.777 2.066 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.TH.05.AA029b10L.JX447033_) Pr(w>1) post mean +- SE for w 11 K 0.793 2.169 +- 0.650 16 S 0.996** 2.494 +- 0.098 21 A 0.815 2.200 +- 0.633 30 G 0.999** 2.499 +- 0.040 41 S 0.850 2.254 +- 0.587 42 F 0.986* 2.478 +- 0.186 44 F 0.941 2.405 +- 0.381 107 L 1.000** 2.500 +- 0.004 266 S 1.000** 2.500 +- 0.011 278 I 0.677 1.989 +- 0.741 305 C 0.552 1.780 +- 0.800 350 A 0.992** 2.487 +- 0.143 354 S 1.000** 2.500 +- 0.020 358 T 0.782 2.147 +- 0.671 388 E 1.000** 2.500 +- 0.004 429 A 0.998** 2.497 +- 0.071 477 Q 1.000** 2.500 +- 0.018 519 A 0.999** 2.499 +- 0.047 595 L 0.994** 2.490 +- 0.127 611 S 0.998** 2.497 +- 0.069 626 H 1.000** 2.500 +- 0.019 634 S 0.899 2.338 +- 0.483 697 S 1.000** 2.500 +- 0.005 720 S 0.948 2.418 +- 0.352 775 V 0.864 2.283 +- 0.548 804 L 0.860 2.273 +- 0.564 827 A 0.688 2.000 +- 0.744