--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 20:44:43 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-DPA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/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 -4005.41 -4044.09 2 -4007.06 -4033.22 -------------------------------------- TOTAL -4005.93 -4043.39 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPA1/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} 1.004965 0.004610 0.879000 1.141000 1.002000 1.001 r(A<->C){all} 0.071255 0.000162 0.048282 0.097858 0.070566 1.000 r(A<->G){all} 0.341388 0.000860 0.284026 0.399771 0.340843 1.001 r(A<->T){all} 0.104146 0.000317 0.071971 0.140879 0.103169 1.001 r(C<->G){all} 0.075597 0.000122 0.055638 0.099142 0.075060 1.000 r(C<->T){all} 0.349116 0.000880 0.292641 0.408073 0.348655 1.002 r(G<->T){all} 0.058497 0.000131 0.037769 0.083020 0.057815 1.000 pi(A){all} 0.212647 0.000161 0.188690 0.238160 0.212224 1.001 pi(C){all} 0.289760 0.000194 0.262968 0.317792 0.289606 1.000 pi(G){all} 0.263707 0.000188 0.237280 0.290920 0.263680 1.000 pi(T){all} 0.233887 0.000169 0.208459 0.259934 0.233922 1.000 alpha{1,2} 0.562699 0.026756 0.334182 0.961066 0.534052 1.000 alpha{3} 15.277322 1282.281681 1.043976 150.291946 2.774631 1.000 pinvar{all} 0.242573 0.006890 0.057877 0.383040 0.250532 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 -3785.131161 Model 7: beta -3804.02363 Model 1: NearlyNeutral -3802.171207 Model 2: PositiveSelection -3785.725264 Model 2 vs 1 32.89188599999943 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_291032.2_HLA-DPA1) Pr(w>1) post mean +- SE for w 36 A 1.000** 11.101 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_291032.2_HLA-DPA1) Pr(w>1) post mean +- SE for w 36 A 1.000** 4.984 +- 1.674 47 F 0.635 3.223 +- 1.929 56 M 0.895 4.455 +- 1.887 90 I 0.735 3.636 +- 1.909 Model 8 vs 7 37.78493800000069 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_291032.2_HLA-DPA1) Pr(w>1) post mean +- SE for w 21 R 0.522 2.346 36 A 1.000** 3.775 47 F 0.867 3.388 56 M 0.978* 3.712 90 I 0.927 3.563 93 N 0.828 3.278 98 L 0.688 2.872 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_291032.2_HLA-DPA1) Pr(w>1) post mean +- SE for w 21 R 0.670 2.643 +- 1.430 36 A 1.000** 3.563 +- 0.706 47 F 0.922 3.346 +- 0.980 56 M 0.988* 3.530 +- 0.757 90 I 0.958* 3.446 +- 0.870 93 N 0.900 3.257 +- 1.007 98 L 0.818 3.013 +- 1.163