--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Feb 12 22:49:27 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_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -30038.49 -30091.34 2 -30046.23 -30085.17 -------------------------------------- TOTAL -30039.18 -30090.65 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.189075 0.009290 3.011557 3.386944 3.185564 1212.34 1248.47 1.000 r(A<->C){all} 0.074695 0.000015 0.067392 0.082392 0.074649 481.89 577.30 1.002 r(A<->G){all} 0.338452 0.000174 0.313705 0.364841 0.338507 357.92 391.29 1.001 r(A<->T){all} 0.032293 0.000006 0.027730 0.037102 0.032160 633.70 721.35 1.001 r(C<->G){all} 0.033943 0.000014 0.026340 0.040936 0.033830 590.08 685.87 1.000 r(C<->T){all} 0.485622 0.000208 0.455758 0.511951 0.485944 403.62 407.79 1.000 r(G<->T){all} 0.034994 0.000011 0.028866 0.041984 0.034890 558.76 597.87 1.000 pi(A){all} 0.409532 0.000051 0.396073 0.423361 0.409460 497.21 530.81 1.000 pi(C){all} 0.170107 0.000033 0.159062 0.181565 0.170054 391.93 448.86 1.000 pi(G){all} 0.209165 0.000034 0.197256 0.219914 0.209206 545.95 566.98 1.000 pi(T){all} 0.211195 0.000036 0.199195 0.222486 0.210963 569.08 611.40 1.000 alpha{1,2} 0.306852 0.000278 0.276167 0.342160 0.305701 897.35 978.45 1.001 alpha{3} 2.515981 0.064464 2.027365 2.989511 2.498368 1176.14 1194.64 1.000 pinvar{all} 0.284499 0.000315 0.250552 0.318349 0.284653 907.58 1043.34 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 -29472.106147 Model 2: PositiveSelection -29397.898141 Model 0: one-ratio -30873.153812 Model 3: discrete -29263.38663 Model 7: beta -29309.268156 Model 8: beta&w>1 -29205.096093 Model 0 vs 1 2802.0953300000037 Model 2 vs 1 148.41601199999423 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 0206.BF.x.LA13BF17.KU168268_) Pr(w>1) post mean +- SE for w 16 P 0.958* 2.779 20 A 0.907 2.684 33 R 0.575 2.069 40 A 0.975* 2.812 41 L 0.995** 2.849 42 S 0.993** 2.845 43 F 0.881 2.636 106 L 1.000** 2.858 264 D 0.999** 2.856 303 S 0.998** 2.854 352 K 1.000** 2.857 386 Q 1.000** 2.857 427 A 0.710 2.319 475 Q 0.921 2.710 498 M 0.872 2.620 517 A 0.839 2.558 593 Q 0.825 2.533 609 S 0.964* 2.790 624 N 1.000** 2.857 695 T 1.000** 2.858 820 S 0.684 2.271 825 A 0.648 2.205 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: 0206.BF.x.LA13BF17.KU168268_) Pr(w>1) post mean +- SE for w 16 P 0.969* 2.464 +- 0.280 20 A 0.940 2.419 +- 0.372 33 R 0.734 2.106 +- 0.670 40 A 0.986* 2.489 +- 0.203 41 L 0.996** 2.504 +- 0.140 42 S 0.996** 2.504 +- 0.142 43 F 0.918 2.386 +- 0.425 106 L 1.000** 2.510 +- 0.101 264 D 0.999** 2.509 +- 0.111 303 S 0.999** 2.508 +- 0.115 352 K 1.000** 2.510 +- 0.104 386 Q 1.000** 2.510 +- 0.105 427 A 0.833 2.256 +- 0.568 475 Q 0.955* 2.442 +- 0.326 498 M 0.953* 2.437 +- 0.328 517 A 0.902 2.362 +- 0.458 518 Q 0.679 2.019 +- 0.701 576 V 0.678 2.018 +- 0.702 593 Q 0.907 2.368 +- 0.448 609 S 0.969* 2.464 +- 0.279 624 N 1.000** 2.510 +- 0.104 695 T 1.000** 2.510 +- 0.101 820 S 0.836 2.260 +- 0.563 825 A 0.826 2.243 +- 0.575 Model 8 vs 7 208.34412599999632 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 0206.BF.x.LA13BF17.KU168268_) Pr(w>1) post mean +- SE for w 16 P 0.997** 2.271 20 A 0.993** 2.265 33 R 0.934 2.171 40 A 0.999** 2.275 41 L 1.000** 2.276 42 S 1.000** 2.276 43 F 0.986* 2.253 106 L 1.000** 2.276 264 D 1.000** 2.276 276 T 0.537 1.544 303 S 1.000** 2.276 348 E 0.582 1.615 352 K 1.000** 2.276 386 Q 1.000** 2.276 427 A 0.973* 2.234 475 Q 0.995** 2.269 498 M 0.998** 2.273 517 A 0.987* 2.255 518 Q 0.974* 2.235 576 V 0.976* 2.237 593 Q 0.989* 2.259 609 S 0.996** 2.269 624 N 1.000** 2.276 695 T 1.000** 2.276 820 S 0.978* 2.241 825 A 0.980* 2.245 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: 0206.BF.x.LA13BF17.KU168268_) Pr(w>1) post mean +- SE for w 16 P 0.992** 2.487 +- 0.143 20 A 0.983* 2.473 +- 0.208 33 R 0.888 2.319 +- 0.511 40 A 0.996** 2.493 +- 0.105 41 L 0.999** 2.498 +- 0.051 42 S 0.999** 2.498 +- 0.059 43 F 0.974* 2.459 +- 0.254 106 L 1.000** 2.500 +- 0.001 264 D 1.000** 2.500 +- 0.024 303 S 1.000** 2.499 +- 0.030 352 K 1.000** 2.500 +- 0.012 386 Q 1.000** 2.500 +- 0.014 427 A 0.938 2.401 +- 0.386 475 Q 0.982* 2.471 +- 0.213 498 M 0.977* 2.464 +- 0.236 517 A 0.969* 2.450 +- 0.278 518 Q 0.768 2.133 +- 0.668 576 V 0.772 2.139 +- 0.664 593 Q 0.960* 2.437 +- 0.310 609 S 0.993** 2.489 +- 0.135 624 N 1.000** 2.500 +- 0.012 695 T 1.000** 2.500 +- 0.001 820 S 0.930 2.388 +- 0.409 825 A 0.925 2.380 +- 0.421