--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 22:33:58 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-DQA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/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 -4577.54 -4610.97 2 -4578.11 -4609.41 -------------------------------------- TOTAL -4577.78 -4610.47 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQA1/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} 1.396605 0.008219 1.233000 1.587000 1.393000 1.001 r(A<->C){all} 0.075266 0.000162 0.052370 0.102518 0.074623 1.000 r(A<->G){all} 0.313963 0.000766 0.261407 0.370456 0.313569 1.000 r(A<->T){all} 0.086774 0.000185 0.062252 0.115067 0.085893 1.000 r(C<->G){all} 0.115818 0.000198 0.089967 0.145236 0.115327 1.001 r(C<->T){all} 0.350246 0.000795 0.296403 0.406707 0.349545 1.000 r(G<->T){all} 0.057933 0.000105 0.039742 0.080026 0.057319 1.000 pi(A){all} 0.222839 0.000170 0.198424 0.248634 0.222540 1.000 pi(C){all} 0.252829 0.000172 0.227537 0.278672 0.252822 1.001 pi(G){all} 0.260793 0.000186 0.234362 0.288173 0.260787 1.000 pi(T){all} 0.263539 0.000182 0.237117 0.290085 0.263282 1.000 alpha{1,2} 0.404651 0.004949 0.297236 0.569814 0.394923 1.000 alpha{3} 2.045586 1.886431 1.045132 4.325206 1.816090 1.000 pinvar{all} 0.114547 0.003484 0.011136 0.232698 0.113230 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 -4422.145612 Model 7: beta -4452.694719 Model 1: NearlyNeutral -4450.300583 Model 2: PositiveSelection -4420.507966 Model 2 vs 1 59.58523400000013 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_002113.2_HLA-DQA1) Pr(w>1) post mean +- SE for w 78 G 1.000** 9.709 90 V 0.752 7.551 91 A 1.000** 9.709 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_002113.2_HLA-DQA1) Pr(w>1) post mean +- SE for w 78 G 1.000** 7.520 +- 1.833 90 V 0.951* 7.128 +- 2.249 91 A 1.000** 7.520 +- 1.833 Model 8 vs 7 61.09821399999964 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_002113.2_HLA-DQA1) Pr(w>1) post mean +- SE for w 78 G 1.000** 8.767 90 V 0.860 7.675 91 A 1.000** 8.767 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_002113.2_HLA-DQA1) Pr(w>1) post mean +- SE for w 41 F 0.799 3.597 +- 1.563 76 K 0.863 3.865 +- 1.470 78 G 1.000** 4.483 +- 1.149 90 V 0.996** 4.464 +- 1.164 91 A 1.000** 4.483 +- 1.149 98 M 0.877 3.913 +- 1.425