--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Apr 12 00:38:25 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-DRB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/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 -3046.22 -3074.68 2 -3046.67 -3070.64 -------------------------------------- TOTAL -3046.42 -3074.00 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB1/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} 0.643768 0.002956 0.544000 0.758000 0.642000 1.000 r(A<->C){all} 0.118655 0.000467 0.079572 0.164732 0.117636 1.000 r(A<->G){all} 0.197078 0.000680 0.149119 0.251845 0.195873 1.000 r(A<->T){all} 0.210508 0.000995 0.152378 0.275912 0.209360 1.000 r(C<->G){all} 0.118134 0.000340 0.084230 0.156392 0.117161 1.000 r(C<->T){all} 0.233516 0.000985 0.176175 0.297884 0.232207 1.000 r(G<->T){all} 0.122109 0.000427 0.084644 0.165890 0.121396 1.000 pi(A){all} 0.217459 0.000182 0.191887 0.244868 0.217195 1.000 pi(C){all} 0.255244 0.000202 0.228017 0.283252 0.254923 1.000 pi(G){all} 0.323233 0.000231 0.293790 0.353179 0.323159 1.000 pi(T){all} 0.204063 0.000168 0.179256 0.230097 0.203913 1.000 alpha{1,2} 0.791847 0.139134 0.363445 1.701675 0.707111 1.001 alpha{3} 3.496540 245.027947 0.505964 12.489141 1.189538 1.000 pinvar{all} 0.511124 0.005041 0.351044 0.628224 0.519164 1.001 --------------------------------------------------------------------------------------------- * 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 -2996.74708 Model 7: beta -3049.409468 Model 1: NearlyNeutral -3047.104289 Model 2: PositiveSelection -2996.103937 Model 2 vs 1 102.00070400000004 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_002115.2_HLA-DRB1) Pr(w>1) post mean +- SE for w 29 S 0.662 4.319 34 P 0.842 5.223 38 W 0.526 3.638 40 P 0.993** 5.978 42 R 1.000** 6.014 55 F 0.525 3.633 57 D 0.990** 5.965 61 Y 0.707 4.543 66 S 0.999** 6.011 76 F 0.573 3.871 86 D 0.985* 5.937 96 I 0.901 5.518 99 Q 0.999** 6.009 100 A 1.000** 6.014 114 V 0.905 5.536 115 V 1.000** 6.014 133 S 0.765 4.838 149 S 0.659 4.304 257 S 0.981* 5.918 258 G 0.744 4.733 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_002115.2_HLA-DRB1) Pr(w>1) post mean +- SE for w 29 S 0.604 4.177 +- 2.697 34 P 0.814 5.386 +- 2.317 40 P 0.992** 6.394 +- 1.207 42 R 1.000** 6.439 +- 1.108 57 D 0.984* 6.341 +- 1.286 61 Y 0.653 4.454 +- 2.659 66 S 0.999** 6.434 +- 1.118 86 D 0.975* 6.285 +- 1.375 96 I 0.845 5.493 +- 2.151 99 Q 0.999** 6.431 +- 1.124 100 A 1.000** 6.439 +- 1.108 114 V 0.880 5.749 +- 2.029 115 V 1.000** 6.439 +- 1.108 133 S 0.723 4.864 +- 2.559 149 S 0.596 4.119 +- 2.689 257 S 0.978* 6.320 +- 1.352 258 G 0.700 4.733 +- 2.602 Model 8 vs 7 105.32477599999947 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_002115.2_HLA-DRB1) Pr(w>1) post mean +- SE for w 29 S 0.708 4.468 34 P 0.865 5.250 38 W 0.626 4.069 40 P 0.994** 5.888 42 R 1.000** 5.917 55 F 0.622 4.050 57 D 0.994** 5.885 61 Y 0.748 4.667 66 S 1.000** 5.915 76 F 0.664 4.256 86 D 0.990** 5.868 96 I 0.931 5.576 99 Q 0.999** 5.913 100 A 1.000** 5.917 114 V 0.924 5.541 115 V 1.000** 5.917 133 S 0.799 4.919 149 S 0.719 4.524 257 S 0.985* 5.841 258 G 0.780 4.828 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_002115.2_HLA-DRB1) Pr(w>1) post mean +- SE for w 3 C 0.556 2.943 +- 1.998 13 T 0.578 3.033 +- 1.992 29 S 0.907 4.380 +- 1.260 33 R 0.770 3.824 +- 1.740 34 P 0.956* 4.582 +- 0.985 38 W 0.924 4.438 +- 1.152 40 P 0.998** 4.751 +- 0.609 42 R 1.000** 4.758 +- 0.585 55 F 0.921 4.426 +- 1.167 57 D 0.999** 4.753 +- 0.599 61 Y 0.920 4.435 +- 1.194 66 S 1.000** 4.758 +- 0.587 76 F 0.930 4.465 +- 1.120 85 P 0.671 3.415 +- 1.913 86 D 0.998** 4.751 +- 0.605 89 Y 0.855 4.158 +- 1.452 96 I 0.987* 4.705 +- 0.719 99 Q 1.000** 4.758 +- 0.587 100 A 1.000** 4.758 +- 0.585 106 T 0.790 3.896 +- 1.651 107 Y 0.821 4.020 +- 1.557 113 G 0.808 3.961 +- 1.578 114 V 0.979* 4.674 +- 0.802 115 V 1.000** 4.758 +- 0.585 119 T 0.725 3.635 +- 1.829 133 S 0.935 4.497 +- 1.114 149 S 0.924 4.448 +- 1.166 178 Q 0.814 3.985 +- 1.563 195 R 0.690 3.487 +- 1.823 257 S 0.995** 4.738 +- 0.648 258 G 0.928 4.471 +- 1.151 262 T 0.760 3.780 +- 1.762 263 G 0.696 3.520 +- 1.880