--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Mar 17 15:12:37 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_A1/ENV_1_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -49724.95 -49772.04 2 -49725.94 -49766.57 -------------------------------------- TOTAL -49725.33 -49771.35 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/ENV_1_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/ENV_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_A1/ENV_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} 8.462852 0.048676 8.059313 8.913363 8.458578 1088.13 1190.79 1.001 r(A<->C){all} 0.134779 0.000025 0.124888 0.144370 0.134708 381.13 420.20 1.002 r(A<->G){all} 0.298388 0.000096 0.279658 0.317868 0.298196 299.48 328.54 1.002 r(A<->T){all} 0.054721 0.000009 0.049071 0.060394 0.054632 506.28 537.13 1.000 r(C<->G){all} 0.079657 0.000026 0.070332 0.089950 0.079573 557.67 614.70 1.000 r(C<->T){all} 0.340936 0.000111 0.320068 0.360484 0.340866 319.88 328.08 1.003 r(G<->T){all} 0.091518 0.000022 0.082686 0.100737 0.091465 458.48 486.47 1.001 pi(A){all} 0.397717 0.000044 0.384921 0.410402 0.397990 423.01 437.26 1.000 pi(C){all} 0.173452 0.000023 0.164095 0.182634 0.173347 283.01 364.68 1.004 pi(G){all} 0.213848 0.000023 0.203784 0.222593 0.213859 636.69 639.63 1.007 pi(T){all} 0.214983 0.000032 0.203765 0.225667 0.214934 394.62 416.75 1.000 alpha{1,2} 0.483987 0.000525 0.440416 0.528128 0.482779 1041.00 1054.31 1.002 alpha{3} 1.058125 0.003776 0.945884 1.184467 1.058257 1163.56 1241.72 1.000 pinvar{all} 0.168000 0.000184 0.142712 0.196071 0.167635 978.20 1109.43 1.002 ------------------------------------------------------------------------------------------------------ * 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 -41777.178034 Model 2: PositiveSelection -41031.166056 Model 0: one-ratio -44475.690467 Model 3: discrete -40991.78024 Model 7: beta -41552.440307 Model 8: beta&w>1 -40894.759678 Model 0 vs 1 5397.024866000007 Model 2 vs 1 1492.02395599999 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.10.DEMB10US011.KC473830_) Pr(w>1) post mean +- SE for w 8 C 0.967* 3.631 69 E 1.000** 3.720 115 E 1.000** 3.720 116 T 1.000** 3.720 117 N 1.000** 3.720 118 T 1.000** 3.720 119 T 1.000** 3.720 120 N 1.000** 3.720 121 A 1.000** 3.720 122 T 1.000** 3.720 123 A 1.000** 3.720 134 D 0.984* 3.678 150 K 0.981* 3.670 153 G 0.998** 3.714 154 N 1.000** 3.720 155 T 1.000** 3.720 174 S 0.999** 3.718 205 N 0.993** 3.702 245 A 0.940 3.558 257 N 1.000** 3.720 272 H 1.000** 3.720 282 A 1.000** 3.720 296 R 1.000** 3.720 297 A 1.000** 3.720 298 Q 1.000** 3.720 301 N 1.000** 3.720 304 Q 0.999** 3.718 305 K 1.000** 3.720 307 A 1.000** 3.720 308 T 1.000** 3.719 311 G 1.000** 3.720 319 S 1.000** 3.720 321 K 1.000** 3.720 322 N 1.000** 3.720 323 S 0.999** 3.717 348 Q 1.000** 3.720 352 R 1.000** 3.720 353 S 1.000** 3.720 354 D 1.000** 3.720 381 K 0.998** 3.716 383 L 1.000** 3.720 401 N 1.000** 3.720 402 D 1.000** 3.720 403 T 1.000** 3.720 404 L 1.000** 3.720 546 N 1.000** 3.720 551 N 0.992** 3.699 557 L 1.000** 3.720 558 S 1.000** 3.720 559 D 1.000** 3.720 578 S 1.000** 3.720 579 I 1.000** 3.720 582 T 1.000** 3.720 589 N 0.981* 3.668 612 D 1.000** 3.720 659 L 1.000** 3.720 661 A 1.000** 3.720 662 P 1.000** 3.720 684 E 1.000** 3.720 688 D 0.995** 3.707 694 F 1.000** 3.720 718 R 0.998** 3.714 723 L 0.784 3.133 763 L 0.778 3.116 764 V 1.000** 3.720 767 I 1.000** 3.720 768 C 1.000** 3.720 772 C 1.000** 3.720 782 A 1.000** 3.720 787 V 0.559 2.522 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.10.DEMB10US011.KC473830_) Pr(w>1) post mean +- SE for w 8 C 0.973* 3.432 +- 0.408 69 E 1.000** 3.500 +- 0.007 115 E 1.000** 3.500 +- 0.000 116 T 1.000** 3.500 +- 0.000 117 N 1.000** 3.500 +- 0.001 118 T 1.000** 3.500 +- 0.000 119 T 1.000** 3.500 +- 0.000 120 N 1.000** 3.500 +- 0.000 121 A 1.000** 3.500 +- 0.000 122 T 1.000** 3.500 +- 0.000 123 A 1.000** 3.500 +- 0.000 134 D 0.988* 3.471 +- 0.269 150 K 0.986* 3.466 +- 0.290 153 G 0.998** 3.496 +- 0.102 154 N 1.000** 3.500 +- 0.001 155 T 1.000** 3.500 +- 0.002 165 V 0.503 2.258 +- 1.250 174 S 0.999** 3.497 +- 0.080 197 T 0.519 2.298 +- 1.249 205 N 0.995** 3.487 +- 0.178 245 A 0.956* 3.390 +- 0.512 257 N 1.000** 3.500 +- 0.017 264 N 0.536 2.340 +- 1.247 272 H 1.000** 3.500 +- 0.007 282 A 1.000** 3.500 +- 0.007 296 R 1.000** 3.500 +- 0.001 297 A 1.000** 3.500 +- 0.000 298 Q 1.000** 3.500 +- 0.002 301 N 1.000** 3.500 +- 0.004 304 Q 0.999** 3.498 +- 0.065 305 K 1.000** 3.500 +- 0.001 307 A 1.000** 3.500 +- 0.001 308 T 1.000** 3.499 +- 0.037 311 G 1.000** 3.500 +- 0.013 319 S 1.000** 3.500 +- 0.000 321 K 1.000** 3.500 +- 0.003 322 N 1.000** 3.500 +- 0.025 323 S 0.999** 3.497 +- 0.092 348 Q 1.000** 3.500 +- 0.003 352 R 1.000** 3.500 +- 0.003 353 S 1.000** 3.500 +- 0.000 354 D 1.000** 3.500 +- 0.000 381 K 0.999** 3.497 +- 0.085 383 L 1.000** 3.500 +- 0.002 401 N 1.000** 3.500 +- 0.001 402 D 1.000** 3.500 +- 0.000 403 T 1.000** 3.500 +- 0.000 404 L 1.000** 3.500 +- 0.002 546 N 1.000** 3.500 +- 0.001 551 N 0.993** 3.483 +- 0.204 557 L 1.000** 3.500 +- 0.000 558 S 1.000** 3.500 +- 0.003 559 D 1.000** 3.500 +- 0.000 578 S 1.000** 3.500 +- 0.000 579 I 1.000** 3.500 +- 0.004 582 T 1.000** 3.500 +- 0.007 589 N 0.986* 3.466 +- 0.291 612 D 1.000** 3.500 +- 0.001 659 L 1.000** 3.500 +- 0.016 661 A 1.000** 3.500 +- 0.020 662 P 1.000** 3.500 +- 0.007 684 E 1.000** 3.500 +- 0.002 688 D 0.997** 3.492 +- 0.145 694 F 1.000** 3.500 +- 0.004 718 R 0.997** 3.494 +- 0.126 723 L 0.831 3.078 +- 0.937 763 L 0.848 3.121 +- 0.897 764 V 1.000** 3.500 +- 0.018 767 I 1.000** 3.500 +- 0.008 768 C 1.000** 3.500 +- 0.008 772 C 1.000** 3.500 +- 0.011 782 A 1.000** 3.500 +- 0.001 787 V 0.657 2.641 +- 1.187 Model 8 vs 7 1315.36125799999 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.10.DEMB10US011.KC473830_) Pr(w>1) post mean +- SE for w 8 C 0.967* 3.144 69 E 1.000** 3.219 115 E 1.000** 3.219 116 T 1.000** 3.219 117 N 1.000** 3.219 118 T 1.000** 3.219 119 T 1.000** 3.219 120 N 1.000** 3.219 121 A 1.000** 3.219 122 T 1.000** 3.219 123 A 1.000** 3.219 134 D 0.978* 3.170 150 K 0.978* 3.169 153 G 0.995** 3.209 154 N 1.000** 3.219 155 T 1.000** 3.219 174 S 0.999** 3.217 205 N 0.991** 3.198 245 A 0.946 3.098 257 N 1.000** 3.219 272 H 1.000** 3.219 282 A 1.000** 3.219 296 R 1.000** 3.219 297 A 1.000** 3.219 298 Q 1.000** 3.219 301 N 1.000** 3.219 304 Q 0.998** 3.216 305 K 1.000** 3.219 307 A 1.000** 3.219 308 T 1.000** 3.218 311 G 1.000** 3.219 319 S 1.000** 3.219 321 K 1.000** 3.219 322 N 1.000** 3.219 323 S 0.999** 3.216 348 Q 1.000** 3.219 352 R 1.000** 3.219 353 S 1.000** 3.219 354 D 1.000** 3.219 381 K 0.997** 3.213 383 L 1.000** 3.219 401 N 1.000** 3.219 402 D 1.000** 3.219 403 T 1.000** 3.219 404 L 1.000** 3.219 546 N 1.000** 3.219 551 N 0.991** 3.199 557 L 1.000** 3.219 558 S 1.000** 3.219 559 D 1.000** 3.219 578 S 1.000** 3.219 579 I 1.000** 3.219 582 T 1.000** 3.219 589 N 0.975* 3.163 612 D 1.000** 3.219 659 L 1.000** 3.219 661 A 1.000** 3.219 662 P 1.000** 3.219 684 E 1.000** 3.219 688 D 0.993** 3.203 694 F 1.000** 3.219 718 R 0.997** 3.213 723 L 0.827 2.826 763 L 0.756 2.667 764 V 1.000** 3.219 767 I 1.000** 3.219 768 C 1.000** 3.219 772 C 1.000** 3.219 782 A 1.000** 3.219 787 V 0.563 2.225 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.10.DEMB10US011.KC473830_) Pr(w>1) post mean +- SE for w 8 C 0.909 3.266 +- 0.740 69 E 1.000** 3.500 +- 0.013 115 E 1.000** 3.500 +- 0.001 116 T 1.000** 3.500 +- 0.001 117 N 1.000** 3.500 +- 0.001 118 T 1.000** 3.500 +- 0.001 119 T 1.000** 3.500 +- 0.001 120 N 1.000** 3.500 +- 0.001 121 A 1.000** 3.500 +- 0.001 122 T 1.000** 3.500 +- 0.001 123 A 1.000** 3.500 +- 0.001 134 D 0.934 3.331 +- 0.636 150 K 0.928 3.316 +- 0.662 153 G 0.986* 3.465 +- 0.298 154 N 1.000** 3.500 +- 0.002 155 T 1.000** 3.500 +- 0.005 174 S 0.998** 3.495 +- 0.114 205 N 0.973* 3.430 +- 0.418 245 A 0.838 3.084 +- 0.946 257 N 1.000** 3.499 +- 0.044 272 H 1.000** 3.500 +- 0.014 282 A 1.000** 3.500 +- 0.015 296 R 1.000** 3.500 +- 0.002 297 A 1.000** 3.500 +- 0.001 298 Q 1.000** 3.500 +- 0.005 301 N 1.000** 3.500 +- 0.009 304 Q 0.996** 3.490 +- 0.162 305 K 1.000** 3.500 +- 0.001 307 A 1.000** 3.500 +- 0.001 308 T 0.999** 3.498 +- 0.080 311 G 1.000** 3.500 +- 0.033 319 S 1.000** 3.500 +- 0.001 321 K 1.000** 3.500 +- 0.008 322 N 0.999** 3.499 +- 0.059 323 S 0.997** 3.493 +- 0.131 348 Q 1.000** 3.500 +- 0.007 352 R 1.000** 3.500 +- 0.009 353 S 1.000** 3.500 +- 0.001 354 D 1.000** 3.500 +- 0.001 381 K 0.991** 3.477 +- 0.241 383 L 1.000** 3.500 +- 0.003 401 N 1.000** 3.500 +- 0.003 402 D 1.000** 3.500 +- 0.001 403 T 1.000** 3.500 +- 0.001 404 L 1.000** 3.500 +- 0.004 546 N 1.000** 3.500 +- 0.001 551 N 0.976* 3.439 +- 0.391 557 L 1.000** 3.500 +- 0.001 558 S 1.000** 3.500 +- 0.008 559 D 1.000** 3.500 +- 0.001 578 S 1.000** 3.500 +- 0.001 579 I 1.000** 3.500 +- 0.007 582 T 1.000** 3.500 +- 0.014 589 N 0.918 3.289 +- 0.705 612 D 1.000** 3.500 +- 0.003 659 L 1.000** 3.500 +- 0.023 661 A 1.000** 3.500 +- 0.036 662 P 1.000** 3.500 +- 0.009 684 E 1.000** 3.500 +- 0.005 688 D 0.977* 3.441 +- 0.385 694 F 1.000** 3.500 +- 0.007 718 R 0.994** 3.486 +- 0.191 723 L 0.598 2.464 +- 1.264 764 V 1.000** 3.499 +- 0.040 767 I 1.000** 3.500 +- 0.013 768 C 1.000** 3.500 +- 0.014 772 C 1.000** 3.500 +- 0.015 782 A 1.000** 3.500 +- 0.002