--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 16:37:27 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-B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-B/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 -4171.12 -4188.03 2 -4171.16 -4187.07 -------------------------------------- TOTAL -4171.14 -4187.66 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-B/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-B/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} 0.627749 0.001702 0.550000 0.712000 0.626000 1.001 r(A<->C){all} 0.134005 0.000360 0.098782 0.172906 0.133211 1.003 r(A<->G){all} 0.284803 0.000745 0.234453 0.340036 0.284435 1.000 r(A<->T){all} 0.154298 0.000751 0.103732 0.210782 0.153062 1.000 r(C<->G){all} 0.100612 0.000168 0.076849 0.127632 0.100068 1.000 r(C<->T){all} 0.219640 0.000647 0.172784 0.272735 0.218589 1.001 r(G<->T){all} 0.106642 0.000313 0.073956 0.143659 0.105904 1.000 pi(A){all} 0.191798 0.000101 0.172470 0.212256 0.191536 1.001 pi(C){all} 0.301237 0.000141 0.278043 0.324580 0.301377 1.000 pi(G){all} 0.336693 0.000151 0.312950 0.361432 0.336605 1.000 pi(T){all} 0.170273 0.000096 0.151698 0.189763 0.170126 1.000 alpha{1,2} 0.598254 0.025826 0.360302 0.978416 0.573430 1.000 alpha{3} 90.738893 3641.074553 3.122157 194.189996 87.289994 1.001 pinvar{all} 0.381108 0.003557 0.250192 0.484477 0.385870 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 -3732.040354 Model 7: beta -3775.537668 Model 1: NearlyNeutral -3766.262518 Model 2: PositiveSelection -3732.126421 Model 2 vs 1 68.27219400000013 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_005505.2_HLA-B) Pr(w>1) post mean +- SE for w 30 Y 0.978* 4.153 32 S 0.534 2.722 45 S 0.863 3.782 66 E 0.935 4.015 73 I 0.935 4.017 84 N 0.948 4.056 87 I 0.978* 4.155 88 Y 0.962* 4.104 90 A 0.725 3.339 91 Q 0.987* 4.184 92 A 0.591 2.878 95 D 0.970* 4.127 98 S 0.797 3.572 101 N 0.580 2.871 116 L 0.874 3.818 118 S 0.933 4.011 135 D 1.000** 4.224 137 Y 0.584 2.883 173 E 0.997** 4.214 177 R 0.999** 4.223 184 E 1.000** 4.224 257 A 0.627 2.998 325 S 0.711 3.277 333 S 0.614 2.953 337 C 0.997** 4.216 340 S 0.688 3.216 341 A 0.591 2.906 344 S 0.590 2.875 347 S 0.627 2.996 350 A 0.960* 4.098 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_005505.2_HLA-B) Pr(w>1) post mean +- SE for w 30 Y 0.979* 4.068 +- 0.824 32 S 0.596 2.770 +- 1.546 45 S 0.876 3.716 +- 1.210 66 E 0.938 3.923 +- 1.005 73 I 0.943 3.948 +- 0.993 84 N 0.953* 3.978 +- 0.950 87 I 0.980* 4.074 +- 0.818 88 Y 0.966* 4.024 +- 0.891 90 A 0.759 3.316 +- 1.430 91 Q 0.988* 4.100 +- 0.774 92 A 0.631 2.872 +- 1.620 95 D 0.972* 4.045 +- 0.860 97 E 0.519 2.507 +- 1.522 98 S 0.818 3.507 +- 1.330 101 N 0.634 2.880 +- 1.514 116 L 0.885 3.740 +- 1.182 118 S 0.939 3.930 +- 1.005 135 D 1.000** 4.138 +- 0.704 137 Y 0.635 2.886 +- 1.519 173 E 0.997** 4.130 +- 0.721 177 R 0.999** 4.137 +- 0.706 184 E 1.000** 4.138 +- 0.703 257 A 0.663 2.986 +- 1.600 325 S 0.740 3.254 +- 1.523 333 S 0.651 2.942 +- 1.607 335 A 0.541 2.559 +- 1.634 337 C 0.997** 4.130 +- 0.719 340 S 0.724 3.199 +- 1.489 341 A 0.641 2.898 +- 1.510 344 S 0.630 2.868 +- 1.619 347 S 0.663 2.983 +- 1.599 350 A 0.965* 4.026 +- 0.898 Model 8 vs 7 86.99462799999947 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_005505.2_HLA-B) Pr(w>1) post mean +- SE for w 30 Y 0.996** 3.827 32 S 0.749 3.054 45 S 0.947 3.674 66 E 0.986* 3.796 73 I 0.982* 3.785 84 N 0.989* 3.806 87 I 0.996** 3.826 88 Y 0.991** 3.813 90 A 0.897 3.520 91 Q 0.998** 3.833 92 A 0.702 2.883 95 D 0.993** 3.819 97 E 0.698 2.897 98 S 0.943 3.664 101 N 0.830 3.312 116 L 0.961* 3.719 118 S 0.984* 3.791 124 V 0.662 2.782 135 D 1.000** 3.839 137 Y 0.806 3.233 142 K 0.604 2.601 152 R 0.605 2.601 173 E 0.999** 3.838 177 R 1.000** 3.839 184 E 1.000** 3.839 257 A 0.732 2.980 325 S 0.800 3.200 333 S 0.722 2.947 335 A 0.614 2.599 337 C 0.999** 3.838 340 S 0.829 3.302 341 A 0.824 3.292 344 S 0.702 2.883 347 S 0.733 2.984 350 A 0.986* 3.795 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_005505.2_HLA-B) Pr(w>1) post mean +- SE for w 30 Y 0.996** 3.579 +- 0.394 32 S 0.829 3.077 +- 1.109 45 S 0.962* 3.474 +- 0.644 66 E 0.989* 3.556 +- 0.457 73 I 0.986* 3.549 +- 0.480 84 N 0.991** 3.563 +- 0.439 87 I 0.996** 3.579 +- 0.395 88 Y 0.993** 3.569 +- 0.425 90 A 0.928 3.375 +- 0.794 91 Q 0.998** 3.584 +- 0.380 92 A 0.781 2.927 +- 1.255 95 D 0.994** 3.573 +- 0.413 97 E 0.798 2.985 +- 1.166 98 S 0.959* 3.466 +- 0.645 101 N 0.886 3.246 +- 0.939 111 A 0.560 2.272 +- 1.458 116 L 0.972* 3.504 +- 0.580 118 S 0.988* 3.553 +- 0.467 124 V 0.772 2.907 +- 1.219 134 H 0.535 2.176 +- 1.497 135 D 1.000** 3.589 +- 0.362 137 Y 0.869 3.194 +- 1.000 142 K 0.738 2.804 +- 1.263 152 R 0.732 2.789 +- 1.280 173 E 0.999** 3.587 +- 0.367 177 R 1.000** 3.589 +- 0.363 184 E 1.000** 3.589 +- 0.362 188 W 0.556 2.258 +- 1.446 257 A 0.804 2.995 +- 1.211 325 S 0.853 3.146 +- 1.092 333 S 0.796 2.972 +- 1.225 335 A 0.716 2.725 +- 1.360 337 C 0.999** 3.588 +- 0.366 340 S 0.880 3.229 +- 0.986 341 A 0.882 3.231 +- 0.957 344 S 0.782 2.927 +- 1.255 347 S 0.805 2.998 +- 1.208 350 A 0.989* 3.557 +- 0.465