--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 23:25:20 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-DQB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/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 -4736.68 -4761.96 2 -4736.88 -4761.25 -------------------------------------- TOTAL -4736.78 -4761.67 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB1/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} 1.494988 0.010048 1.309000 1.700000 1.491000 1.000 r(A<->C){all} 0.097590 0.000215 0.070585 0.128878 0.096899 1.000 r(A<->G){all} 0.243611 0.000553 0.198660 0.291292 0.243298 1.000 r(A<->T){all} 0.111080 0.000331 0.078093 0.149320 0.110091 1.000 r(C<->G){all} 0.084797 0.000125 0.064467 0.108281 0.084417 1.001 r(C<->T){all} 0.371739 0.000831 0.317460 0.429537 0.371334 1.000 r(G<->T){all} 0.091182 0.000178 0.067025 0.118903 0.090761 1.000 pi(A){all} 0.213236 0.000168 0.188748 0.239925 0.212889 1.000 pi(C){all} 0.274979 0.000181 0.248934 0.301305 0.274816 1.001 pi(G){all} 0.310196 0.000195 0.282973 0.338299 0.310011 1.001 pi(T){all} 0.201590 0.000154 0.177545 0.227012 0.201313 1.000 alpha{1,2} 0.403163 0.004423 0.297946 0.554992 0.395285 1.000 alpha{3} 2.578861 30.190802 1.108606 5.598211 2.025743 1.000 pinvar{all} 0.138659 0.003439 0.022964 0.251119 0.140871 1.000 --------------------------------------------------------------------------------------------- * 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 -4412.629266 Model 7: beta -4444.988725 Model 1: NearlyNeutral -4437.31931 Model 2: PositiveSelection -4417.335403 Model 2 vs 1 39.967813999999635 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_002114.3_HLA-DQB1) Pr(w>1) post mean +- SE for w 15 V 0.592 2.237 40 F 0.912 2.908 44 G 0.937 2.961 57 L 1.000** 3.092 68 Y 0.818 2.711 88 D 0.997** 3.086 98 V 0.614 2.285 101 G 0.904 2.891 102 T 0.933 2.952 107 R 0.981* 3.051 112 V 0.838 2.753 114 F 0.858 2.795 116 G 0.835 2.746 121 R 0.510 2.037 194 R 0.648 2.354 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_002114.3_HLA-DQB1) Pr(w>1) post mean +- SE for w 15 V 0.607 2.286 +- 1.113 40 F 0.909 2.953 +- 0.784 44 G 0.937 3.021 +- 0.720 57 L 1.000** 3.157 +- 0.513 68 Y 0.809 2.716 +- 0.951 88 D 0.997** 3.152 +- 0.524 98 V 0.611 2.265 +- 1.084 101 G 0.899 2.925 +- 0.806 102 T 0.930 3.001 +- 0.736 107 R 0.980* 3.118 +- 0.589 112 V 0.840 2.802 +- 0.914 114 F 0.856 2.835 +- 0.886 116 G 0.828 2.763 +- 0.926 121 R 0.525 2.078 +- 1.192 194 R 0.665 2.421 +- 1.095 Model 8 vs 7 64.71891800000049 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_002114.3_HLA-DQB1) Pr(w>1) post mean +- SE for w 8 R 0.754 2.055 15 V 0.871 2.268 40 F 0.995** 2.503 44 G 0.995** 2.503 57 L 1.000** 2.512 68 Y 0.987* 2.489 69 A 0.869 2.271 86 R 0.725 1.998 88 D 1.000** 2.512 98 V 0.959* 2.437 101 G 0.995** 2.503 102 T 0.996** 2.504 107 R 0.998** 2.509 112 V 0.980* 2.476 113 A 0.616 1.795 114 F 0.986* 2.487 115 R 0.799 2.140 116 G 0.988* 2.491 117 I 0.654 1.870 121 R 0.714 1.948 169 V 0.705 1.951 194 R 0.891 2.306 247 R 0.657 1.858 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_002114.3_HLA-DQB1) Pr(w>1) post mean +- SE for w 15 V 0.723 2.130 +- 0.917 40 F 0.970* 2.626 +- 0.491 44 G 0.976* 2.639 +- 0.476 57 L 1.000** 2.684 +- 0.390 68 Y 0.932 2.549 +- 0.586 69 A 0.637 1.953 +- 0.903 88 D 0.999** 2.682 +- 0.393 98 V 0.830 2.338 +- 0.757 101 G 0.968* 2.622 +- 0.495 102 T 0.976* 2.638 +- 0.474 107 R 0.991** 2.668 +- 0.424 112 V 0.927 2.544 +- 0.608 114 F 0.940 2.568 +- 0.574 115 R 0.535 1.747 +- 0.916 116 G 0.939 2.563 +- 0.572 121 R 0.564 1.786 +- 1.052 194 R 0.762 2.214 +- 0.886