--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Feb 11 13:36:11 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_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -32411.62 -32455.16 2 -32412.44 -32451.69 -------------------------------------- TOTAL -32411.95 -32454.50 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 4.412408 0.021471 4.145539 4.711587 4.409860 663.62 705.10 1.000 r(A<->C){all} 0.073778 0.000014 0.066835 0.080844 0.073671 646.73 682.76 1.000 r(A<->G){all} 0.346123 0.000178 0.319883 0.371248 0.346186 356.69 404.03 1.002 r(A<->T){all} 0.034767 0.000007 0.030161 0.040460 0.034644 689.19 692.07 1.000 r(C<->G){all} 0.040412 0.000016 0.032595 0.048187 0.040191 646.37 720.41 1.000 r(C<->T){all} 0.462400 0.000205 0.435443 0.491306 0.462243 352.86 393.69 1.002 r(G<->T){all} 0.042520 0.000013 0.035538 0.049704 0.042426 749.95 836.96 1.000 pi(A){all} 0.417173 0.000051 0.402278 0.430204 0.417234 429.63 474.45 1.000 pi(C){all} 0.175578 0.000027 0.164797 0.184846 0.175477 462.58 552.23 1.001 pi(G){all} 0.203208 0.000033 0.193026 0.215333 0.203088 496.46 612.03 1.000 pi(T){all} 0.204042 0.000032 0.193506 0.215355 0.204010 680.97 682.94 1.000 alpha{1,2} 0.298749 0.000226 0.268436 0.327047 0.298491 941.75 1131.59 1.000 alpha{3} 2.193268 0.043366 1.819823 2.619593 2.185551 1180.09 1224.23 1.000 pinvar{all} 0.238728 0.000304 0.203745 0.271047 0.238809 900.61 956.17 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 -31434.778169 Model 2: PositiveSelection -31345.916802 Model 0: one-ratio -33050.813068 Model 3: discrete -31176.003452 Model 7: beta -31228.681779 Model 8: beta&w>1 -31116.540357 Model 0 vs 1 3232.069798000004 Model 2 vs 1 177.72273400000267 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.BR.10.10BR_PE019.KT427740_) Pr(w>1) post mean +- SE for w 17 S 0.990* 3.165 32 A 0.905 2.979 36 L 0.999** 3.186 37 N 0.559 2.222 101 P 1.000** 3.188 260 E 0.962* 3.103 348 Q 0.961* 3.102 382 K 1.000** 3.188 423 T 0.673 2.472 471 Q 1.000** 3.187 513 S 0.891 2.949 589 L 0.938 3.052 605 P 0.997** 3.181 620 H 0.988* 3.161 691 S 1.000** 3.188 798 I 0.938 3.051 816 S 0.958* 3.097 821 N 1.000** 3.188 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.BR.10.10BR_PE019.KT427740_) Pr(w>1) post mean +- SE for w 17 S 0.994** 3.271 +- 0.445 32 A 0.940 3.141 +- 0.675 35 S 0.534 2.192 +- 1.160 36 L 0.999** 3.282 +- 0.415 37 N 0.638 2.403 +- 1.119 101 P 1.000** 3.283 +- 0.412 131 L 0.515 2.131 +- 1.146 260 E 0.975* 3.224 +- 0.541 348 Q 0.976* 3.227 +- 0.537 382 K 1.000** 3.283 +- 0.412 423 T 0.766 2.722 +- 1.025 471 Q 1.000** 3.283 +- 0.413 513 S 0.935 3.132 +- 0.690 589 L 0.963* 3.197 +- 0.591 605 P 0.998** 3.280 +- 0.422 620 H 0.993** 3.267 +- 0.453 628 L 0.529 2.140 +- 1.130 691 S 1.000** 3.283 +- 0.412 798 I 0.966* 3.204 +- 0.581 816 S 0.972* 3.217 +- 0.553 821 N 1.000** 3.283 +- 0.412 Model 8 vs 7 224.28284399999393 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.BR.10.10BR_PE019.KT427740_) Pr(w>1) post mean +- SE for w 5 T 0.636 1.567 17 S 1.000** 2.088 18 S 0.530 1.413 21 T 0.936 1.996 28 R 0.759 1.743 30 D 0.966* 2.039 32 A 0.998** 2.086 35 S 0.911 1.960 36 L 1.000** 2.089 37 N 0.994** 2.080 38 L 0.572 1.470 99 Q 0.501 1.368 101 P 1.000** 2.089 131 L 0.948 2.014 260 E 1.000** 2.088 348 Q 1.000** 2.088 382 K 1.000** 2.089 423 T 0.992** 2.077 471 Q 1.000** 2.089 483 F 0.888 1.928 494 M 0.987* 2.070 513 S 0.996** 2.083 514 T 0.731 1.702 523 I 0.915 1.967 572 A 0.699 1.657 589 L 0.999** 2.087 605 P 1.000** 2.088 620 H 1.000** 2.088 628 L 0.990* 2.074 691 S 1.000** 2.089 769 I 0.646 1.580 798 I 0.998** 2.086 816 S 1.000** 2.088 821 N 1.000** 2.089 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.BR.10.10BR_PE019.KT427740_) Pr(w>1) post mean +- SE for w 17 S 0.998** 2.496 +- 0.075 21 T 0.786 2.154 +- 0.666 30 D 0.618 1.892 +- 0.776 32 A 0.984* 2.475 +- 0.197 35 S 0.821 2.207 +- 0.629 36 L 1.000** 2.500 +- 0.027 37 N 0.917 2.368 +- 0.440 101 P 1.000** 2.500 +- 0.001 131 L 0.813 2.199 +- 0.631 260 E 0.993** 2.489 +- 0.129 348 Q 0.993** 2.489 +- 0.131 382 K 1.000** 2.500 +- 0.001 423 T 0.947 2.415 +- 0.359 471 Q 1.000** 2.500 +- 0.013 483 F 0.582 1.825 +- 0.800 494 M 0.558 1.801 +- 0.787 513 S 0.982* 2.471 +- 0.215 523 I 0.549 1.775 +- 0.803 589 L 0.986* 2.477 +- 0.188 605 P 0.999** 2.499 +- 0.047 620 H 0.997** 2.495 +- 0.087 628 L 0.883 2.313 +- 0.513 691 S 1.000** 2.500 +- 0.001 798 I 0.986* 2.478 +- 0.184 816 S 0.993** 2.489 +- 0.131 821 N 1.000** 2.500 +- 0.003