--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Feb 12 06:04:32 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_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -32200.00 -32240.54 2 -32197.19 -32237.04 -------------------------------------- TOTAL -32197.82 -32239.88 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_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_N2/POL_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} 4.528076 0.022500 4.238315 4.825170 4.521645 514.52 782.28 1.000 r(A<->C){all} 0.080871 0.000015 0.073167 0.088600 0.080777 794.03 809.91 1.000 r(A<->G){all} 0.346356 0.000178 0.317368 0.371422 0.346772 289.45 307.69 1.000 r(A<->T){all} 0.034837 0.000006 0.030259 0.039725 0.034722 616.54 680.57 1.000 r(C<->G){all} 0.036741 0.000016 0.029067 0.044800 0.036634 511.65 592.14 1.001 r(C<->T){all} 0.464710 0.000202 0.435600 0.491353 0.464635 255.63 275.82 1.000 r(G<->T){all} 0.036485 0.000011 0.030119 0.042840 0.036431 824.78 828.67 1.000 pi(A){all} 0.419994 0.000049 0.406275 0.433531 0.419819 440.95 517.53 1.000 pi(C){all} 0.168446 0.000028 0.157954 0.178537 0.168374 446.19 449.13 1.000 pi(G){all} 0.204878 0.000028 0.194317 0.214761 0.204916 498.39 563.89 1.000 pi(T){all} 0.206683 0.000034 0.196076 0.218470 0.206542 430.76 492.63 1.000 alpha{1,2} 0.267239 0.000161 0.240936 0.290561 0.267113 1097.08 1144.55 1.000 alpha{3} 2.485673 0.051842 2.070056 2.943386 2.472733 1256.15 1288.56 1.000 pinvar{all} 0.232979 0.000262 0.201076 0.264822 0.233068 627.89 869.74 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 -31020.236433 Model 2: PositiveSelection -30867.336546 Model 0: one-ratio -32712.450941 Model 3: discrete -30685.050346 Model 7: beta -30804.215158 Model 8: beta&w>1 -30631.594021 Model 0 vs 1 3384.429016000002 Model 2 vs 1 305.79977399999916 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: B.US.11.AMBI_CLONE.KU641402_) Pr(w>1) post mean +- SE for w 17 P 1.000** 4.215 32 T 1.000** 4.215 33 F 0.998** 4.210 98 S 1.000** 4.215 344 R 0.999** 4.212 378 V 1.000** 4.215 419 A 0.994** 4.194 467 Q 1.000** 4.215 509 A 0.994** 4.196 601 S 1.000** 4.215 616 H 0.998** 4.210 687 T 1.000** 4.215 812 S 1.000** 4.215 817 T 1.000** 4.215 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: B.US.11.AMBI_CLONE.KU641402_) Pr(w>1) post mean +- SE for w 17 P 1.000** 3.685 +- 0.389 32 T 1.000** 3.685 +- 0.389 33 F 0.999** 3.684 +- 0.393 98 S 1.000** 3.685 +- 0.389 256 D 0.695 2.797 +- 1.212 344 R 1.000** 3.684 +- 0.391 378 V 1.000** 3.685 +- 0.389 419 A 0.998** 3.679 +- 0.408 467 Q 1.000** 3.685 +- 0.389 490 V 0.649 2.637 +- 1.210 509 A 0.998** 3.679 +- 0.407 510 T 0.721 2.827 +- 1.145 601 S 1.000** 3.685 +- 0.389 616 H 1.000** 3.684 +- 0.393 624 L 0.661 2.688 +- 1.224 687 T 1.000** 3.685 +- 0.389 812 S 1.000** 3.685 +- 0.389 817 T 1.000** 3.685 +- 0.389 Model 8 vs 7 345.24227399999654 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: B.US.11.AMBI_CLONE.KU641402_) Pr(w>1) post mean +- SE for w 17 P 1.000** 2.643 30 Q 0.746 2.143 32 T 1.000** 2.643 33 F 1.000** 2.643 35 F 0.619 1.890 72 S 0.875 2.397 98 S 1.000** 2.643 256 D 0.990** 2.624 344 R 1.000** 2.643 378 V 1.000** 2.643 419 A 1.000** 2.643 467 Q 1.000** 2.643 490 V 0.999** 2.641 509 A 1.000** 2.643 510 T 0.999** 2.642 568 V 0.987* 2.618 585 L 0.953* 2.551 601 S 1.000** 2.643 616 H 1.000** 2.643 624 L 0.993** 2.629 687 T 1.000** 2.643 765 V 0.957* 2.558 767 L 0.803 2.254 812 S 1.000** 2.643 817 T 1.000** 2.643 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: B.US.11.AMBI_CLONE.KU641402_) Pr(w>1) post mean +- SE for w 17 P 1.000** 2.524 +- 0.152 21 A 0.537 1.735 +- 0.833 30 Q 0.745 2.088 +- 0.717 32 T 1.000** 2.524 +- 0.152 33 F 1.000** 2.523 +- 0.153 35 F 0.689 1.991 +- 0.774 72 S 0.744 2.093 +- 0.697 98 S 1.000** 2.524 +- 0.152 256 D 0.972* 2.474 +- 0.300 344 R 1.000** 2.524 +- 0.152 378 V 1.000** 2.524 +- 0.152 419 A 0.999** 2.523 +- 0.156 467 Q 1.000** 2.524 +- 0.152 490 V 0.980* 2.484 +- 0.252 509 A 0.999** 2.523 +- 0.156 510 T 0.986* 2.495 +- 0.226 568 V 0.918 2.374 +- 0.439 585 L 0.899 2.347 +- 0.494 601 S 1.000** 2.524 +- 0.152 616 H 1.000** 2.523 +- 0.153 624 L 0.973* 2.474 +- 0.293 687 T 1.000** 2.524 +- 0.152 765 V 0.918 2.380 +- 0.457 767 L 0.842 2.251 +- 0.626 794 L 0.520 1.705 +- 0.840 812 S 1.000** 2.524 +- 0.152 817 T 1.000** 2.524 +- 0.152