--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Feb 10 23:10:08 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_2/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -30003.54 -30045.47 2 -30005.35 -30046.08 -------------------------------------- TOTAL -30004.08 -30045.82 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N2/POL_1_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N2/POL_1_2/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_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.120844 0.007473 2.950945 3.289556 3.118392 1167.33 1206.02 1.000 r(A<->C){all} 0.077608 0.000016 0.069511 0.085079 0.077500 657.56 717.87 1.000 r(A<->G){all} 0.345174 0.000152 0.321095 0.368907 0.345328 309.57 401.82 1.002 r(A<->T){all} 0.033282 0.000005 0.028743 0.037685 0.033200 593.55 786.45 1.000 r(C<->G){all} 0.040371 0.000017 0.032272 0.048584 0.040184 698.10 732.12 1.001 r(C<->T){all} 0.462310 0.000178 0.436367 0.488444 0.462479 363.85 441.23 1.001 r(G<->T){all} 0.041256 0.000013 0.035061 0.048820 0.041127 730.29 803.33 1.000 pi(A){all} 0.410060 0.000050 0.395844 0.422988 0.410183 791.09 867.55 1.000 pi(C){all} 0.169847 0.000030 0.158516 0.180136 0.169835 603.97 626.13 1.002 pi(G){all} 0.203739 0.000029 0.193303 0.214697 0.203627 608.08 715.16 1.000 pi(T){all} 0.216353 0.000036 0.204959 0.228330 0.216299 762.62 798.84 1.000 alpha{1,2} 0.289572 0.000206 0.263101 0.318406 0.288809 889.74 994.56 1.000 alpha{3} 2.404885 0.060077 1.939702 2.864435 2.387794 1179.84 1245.41 1.000 pinvar{all} 0.266603 0.000297 0.233151 0.299325 0.266780 940.60 1053.83 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 -29370.480694 Model 2: PositiveSelection -29291.241634 Model 0: one-ratio -30818.626155 Model 3: discrete -29164.468606 Model 7: beta -29225.191414 Model 8: beta&w>1 -29118.940595 Model 0 vs 1 2896.290922 Model 2 vs 1 158.47811999999976 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.00.ES1_20.EF363123_) Pr(w>1) post mean +- SE for w 17 S 0.919 2.792 33 S 0.993** 2.937 34 L 1.000** 2.951 41 T 0.953* 2.859 42 L 0.985* 2.923 43 S 0.960* 2.874 54 L 0.851 2.661 107 P 1.000** 2.951 266 E 1.000** 2.951 278 T 0.719 2.403 305 S 0.865 2.688 350 Q 0.591 2.153 354 K 0.988* 2.927 388 V 0.767 2.497 429 T 0.614 2.198 519 T 0.542 2.057 611 S 0.947 2.847 626 H 1.000** 2.951 697 A 1.000** 2.951 775 I 0.902 2.761 804 I 0.978* 2.909 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.00.ES1_20.EF363123_) Pr(w>1) post mean +- SE for w 17 S 0.949 2.441 +- 0.360 21 T 0.544 1.821 +- 0.755 32 R 0.825 2.241 +- 0.573 33 S 0.992** 2.507 +- 0.191 34 L 1.000** 2.519 +- 0.137 41 T 0.978* 2.486 +- 0.258 42 L 0.990** 2.504 +- 0.203 43 S 0.981* 2.490 +- 0.248 54 L 0.908 2.379 +- 0.458 107 P 1.000** 2.519 +- 0.137 266 E 1.000** 2.519 +- 0.137 278 T 0.921 2.390 +- 0.418 305 S 0.952* 2.442 +- 0.347 350 Q 0.825 2.246 +- 0.582 354 K 0.993** 2.508 +- 0.186 388 V 0.894 2.355 +- 0.482 429 T 0.796 2.205 +- 0.619 503 A 0.686 2.036 +- 0.706 519 T 0.742 2.123 +- 0.670 611 S 0.960* 2.459 +- 0.325 626 H 1.000** 2.519 +- 0.137 660 L 0.580 1.873 +- 0.745 697 A 1.000** 2.519 +- 0.137 775 I 0.952* 2.445 +- 0.351 804 I 0.985* 2.496 +- 0.229 826 T 0.726 2.094 +- 0.675 Model 8 vs 7 212.50163800000155 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.00.ES1_20.EF363123_) Pr(w>1) post mean +- SE for w 5 N 0.945 1.963 12 K 0.678 1.594 16 L 0.688 1.607 17 S 0.996** 2.033 21 T 0.912 1.917 32 R 0.998** 2.036 33 S 0.999** 2.038 34 L 1.000** 2.039 41 T 0.999** 2.038 42 L 1.000** 2.038 43 S 0.999** 2.038 44 F 0.783 1.736 54 L 0.988* 2.023 81 N 0.853 1.836 107 P 1.000** 2.039 137 I 0.523 1.378 266 E 1.000** 2.039 278 T 0.999** 2.038 305 S 0.999** 2.037 350 Q 0.993** 2.029 354 K 1.000** 2.038 357 F 0.631 1.527 388 V 0.995** 2.032 420 R 0.906 1.910 429 T 0.981* 2.012 477 Q 0.886 1.881 503 A 0.965* 1.990 519 T 0.969* 1.995 520 T 0.948 1.967 578 V 0.930 1.942 595 S 0.915 1.921 611 S 0.996** 2.034 626 H 1.000** 2.039 660 L 0.952* 1.973 674 I 0.508 1.353 697 A 1.000** 2.039 731 L 0.543 1.390 775 I 0.998** 2.036 777 L 0.755 1.695 804 I 0.999** 2.038 826 T 0.985* 2.018 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.00.ES1_20.EF363123_) Pr(w>1) post mean +- SE for w 17 S 0.985* 2.476 +- 0.196 21 T 0.740 2.077 +- 0.717 32 R 0.866 2.288 +- 0.538 33 S 0.998** 2.497 +- 0.063 34 L 1.000** 2.500 +- 0.001 41 T 0.991** 2.486 +- 0.146 42 L 0.997** 2.495 +- 0.088 43 S 0.993** 2.488 +- 0.135 44 F 0.574 1.796 +- 0.823 54 L 0.965* 2.444 +- 0.295 107 P 1.000** 2.500 +- 0.002 266 E 1.000** 2.500 +- 0.001 278 T 0.947 2.417 +- 0.351 305 S 0.977* 2.464 +- 0.237 350 Q 0.897 2.337 +- 0.482 354 K 0.998** 2.496 +- 0.075 388 V 0.953* 2.425 +- 0.337 429 T 0.915 2.364 +- 0.448 503 A 0.843 2.247 +- 0.587 519 T 0.887 2.318 +- 0.512 595 S 0.523 1.733 +- 0.807 611 S 0.990* 2.483 +- 0.163 626 H 1.000** 2.500 +- 0.003 660 L 0.717 2.044 +- 0.726 697 A 1.000** 2.500 +- 0.004 775 I 0.983* 2.472 +- 0.208 777 L 0.620 1.864 +- 0.818 804 I 0.996** 2.493 +- 0.105 826 T 0.844 2.251 +- 0.580