--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Apr 12 00:46:37 WEST 2018 codeml.models=1 2 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir= input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir= tcoffee.dir= tcoffee.minScore=3 input.fasta= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DRB3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -1980.50 -1997.15 2 -1980.38 -1998.75 -------------------------------------- TOTAL -1980.44 -1998.24 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DRB3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Summaries are based on a total of 15002 samples from 2 runs) (Each run produced 10001 samples of which 7501 samples were included) 95% Cred. Interval ---------------------- Parameter Mean Variance Lower Upper Median PSRF * --------------------------------------------------------------------------------------------- TL{all} 0.265317 0.000885 0.212000 0.329000 0.263000 1.000 r(A<->C){all} 0.101350 0.000840 0.051181 0.164004 0.098791 1.000 r(A<->G){all} 0.168862 0.001157 0.109084 0.242242 0.166530 1.000 r(A<->T){all} 0.210862 0.002079 0.129527 0.306510 0.208112 1.000 r(C<->G){all} 0.094341 0.000483 0.056313 0.141940 0.092704 1.000 r(C<->T){all} 0.340278 0.002551 0.245988 0.442625 0.338700 1.000 r(G<->T){all} 0.084306 0.000597 0.042649 0.137257 0.082479 1.002 pi(A){all} 0.216659 0.000197 0.189988 0.244904 0.216516 1.000 pi(C){all} 0.261869 0.000218 0.233643 0.291465 0.261522 1.000 pi(G){all} 0.316085 0.000245 0.286490 0.346889 0.315873 1.000 pi(T){all} 0.205388 0.000185 0.179485 0.232576 0.205199 1.000 alpha{1,2} 28.084679 2735.050281 0.173688 179.276444 0.846342 1.003 alpha{3} 100.482318 3261.914324 7.034359 194.807984 99.861952 1.000 pinvar{all} 0.694802 0.009037 0.471945 0.815786 0.712470 1.003 --------------------------------------------------------------------------------------------- * Convergence diagnostic (PSRF = Potential scale reduction factor [Gelman and Rubin, 1992], uncorrected) should approach 1 as runs converge. The values may be unreliable if you have a small number of samples. PSRF should only be used as a rough guide to convergence since all the assumptions that allow one to interpret it as a scale reduction factor are not met in the phylogenetic context. --- CODEML SUMMARY Model 8: beta&w>1 -1807.692703 Model 7: beta -1836.888718 Model 1: NearlyNeutral -1836.836979 Model 2: PositiveSelection -1807.692074 Model 2 vs 1 58.28980999999976 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_072049.2_HLA-DRB3) Pr(w>1) post mean +- SE for w 28 L 0.954* 7.852 29 R 1.000** 8.181 31 S 0.803 6.768 46 D 0.973* 7.987 50 H 0.682 5.897 55 F 1.000** 8.179 56 L 0.549 4.940 75 V 0.999** 8.175 85 L 1.000** 8.181 92 R 0.931 7.686 104 G 0.953* 7.841 122 A 0.773 6.548 138 S 0.925 7.641 205 E 0.585 5.201 245 H 0.720 6.169 246 S 0.963* 7.915 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: Homo_sapiens_Hominidae_Haplorrhini_NP_072049.2_HLA-DRB3) Pr(w>1) post mean +- SE for w 28 L 0.957* 7.475 +- 2.185 29 R 1.000** 7.800 +- 1.733 31 S 0.823 6.506 +- 3.010 46 D 0.974* 7.601 +- 2.024 50 H 0.717 5.702 +- 3.311 55 F 1.000** 7.799 +- 1.736 56 L 0.609 4.832 +- 3.349 75 V 0.999** 7.794 +- 1.744 85 L 1.000** 7.800 +- 1.733 92 R 0.935 7.304 +- 2.363 104 G 0.957* 7.489 +- 2.189 122 A 0.796 6.305 +- 3.109 138 S 0.931 7.297 +- 2.396 205 E 0.635 5.080 +- 3.402 245 H 0.747 5.870 +- 3.203 246 S 0.966* 7.559 +- 2.107 Model 8 vs 7 58.39202999999998 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_072049.2_HLA-DRB3) Pr(w>1) post mean +- SE for w 28 L 0.955* 7.817 29 R 1.000** 8.141 31 S 0.805 6.746 46 D 0.973* 7.950 50 H 0.684 5.888 55 F 1.000** 8.139 56 L 0.553 4.948 75 V 0.999** 8.135 85 L 1.000** 8.141 92 R 0.932 7.654 104 G 0.953* 7.805 122 A 0.774 6.530 138 S 0.925 7.608 205 E 0.588 5.202 245 H 0.723 6.162 246 S 0.963* 7.878 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: Homo_sapiens_Hominidae_Haplorrhini_NP_072049.2_HLA-DRB3) Pr(w>1) post mean +- SE for w 14 R 0.607 3.608 +- 2.669 18 A 0.521 3.120 +- 2.659 22 R 0.648 3.846 +- 2.652 23 P 0.604 3.590 +- 2.670 24 R 0.529 3.168 +- 2.663 28 L 0.992** 5.888 +- 1.485 29 R 1.000** 5.940 +- 1.431 31 S 0.939 5.562 +- 1.817 44 Y 0.749 4.364 +- 2.329 46 D 0.996** 5.914 +- 1.457 50 H 0.903 5.322 +- 1.965 55 F 1.000** 5.940 +- 1.431 56 L 0.898 5.246 +- 1.910 75 V 1.000** 5.939 +- 1.432 78 S 0.781 4.551 +- 2.275 85 L 1.000** 5.940 +- 1.431 86 L 0.735 4.283 +- 2.352 88 Q 0.590 3.478 +- 2.465 89 K 0.523 3.121 +- 2.458 92 R 0.988* 5.861 +- 1.508 99 H 0.630 3.693 +- 2.452 102 G 0.549 3.261 +- 2.470 104 G 0.989* 5.872 +- 1.515 122 A 0.930 5.502 +- 1.859 131 N 0.645 3.773 +- 2.441 138 S 0.983* 5.833 +- 1.552 153 G 0.668 3.903 +- 2.424 184 R 0.678 3.966 +- 2.425 201 A 0.569 3.394 +- 2.672 205 E 0.872 5.120 +- 2.066 209 R 0.725 4.225 +- 2.361 245 H 0.940 5.531 +- 1.756 246 S 0.990* 5.879 +- 1.512 247 G 0.704 4.159 +- 2.574