--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 16:41:35 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-C/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-C/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 -2201.93 -2212.00 2 -2201.72 -2211.50 -------------------------------------- TOTAL -2201.82 -2211.78 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-C/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-C/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} 0.153378 0.000348 0.121000 0.194000 0.152000 1.000 r(A<->C){all} 0.174749 0.001467 0.107554 0.255721 0.172343 1.000 r(A<->G){all} 0.324630 0.002602 0.230865 0.431846 0.322444 1.001 r(A<->T){all} 0.093258 0.001647 0.026583 0.182979 0.089277 1.000 r(C<->G){all} 0.066932 0.000408 0.032570 0.111913 0.065296 1.001 r(C<->T){all} 0.248857 0.002409 0.160052 0.351556 0.245570 1.000 r(G<->T){all} 0.091573 0.000899 0.041045 0.157659 0.088704 1.000 pi(A){all} 0.198705 0.000134 0.176542 0.221935 0.198423 1.000 pi(C){all} 0.308291 0.000181 0.282091 0.334931 0.308300 1.000 pi(G){all} 0.336199 0.000192 0.309184 0.363398 0.336024 1.000 pi(T){all} 0.156804 0.000112 0.136500 0.178466 0.156590 1.000 alpha{1,2} 82.406501 4003.004596 0.372055 193.337012 77.504659 1.002 alpha{3} 103.533438 3171.092922 9.735424 195.283904 103.721452 1.001 pinvar{all} 0.777500 0.003801 0.615880 0.847185 0.790397 1.002 --------------------------------------------------------------------------------------------- * 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 -2152.118753 Model 7: beta -2165.809291 Model 1: NearlyNeutral -2165.808156 Model 2: PositiveSelection -2152.140463 Model 2 vs 1 27.335385999999744 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_002108.4_HLA-C) Pr(w>1) post mean +- SE for w 48 S 0.866 10.052 97 A 0.983* 11.280 104 N 0.548 6.705 121 R 0.995** 11.403 138 D 0.938 10.809 140 S 0.860 9.993 171 L 0.574 6.984 180 L 0.989* 11.342 187 T 0.991** 11.360 329 A 0.813 9.495 362 T 0.814 9.500 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_002108.4_HLA-C) Pr(w>1) post mean +- SE for w 48 S 0.866 7.729 +- 3.045 97 A 0.980* 8.636 +- 1.860 104 N 0.622 5.727 +- 4.002 121 R 0.994** 8.743 +- 1.630 138 D 0.958* 8.451 +- 2.159 140 S 0.899 7.980 +- 2.759 171 L 0.671 6.115 +- 3.892 180 L 0.987* 8.692 +- 1.744 187 T 0.991** 8.719 +- 1.683 329 A 0.828 7.418 +- 3.289 362 T 0.829 7.426 +- 3.283 Model 8 vs 7 27.381075999999666 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_002108.4_HLA-C) Pr(w>1) post mean +- SE for w 48 S 0.874 10.006 97 A 0.986* 11.184 104 N 0.558 6.679 121 R 0.996** 11.290 138 D 0.954* 10.844 140 S 0.882 10.092 171 L 0.590 7.019 180 L 0.991** 11.236 187 T 0.993** 11.259 329 A 0.823 9.473 362 T 0.824 9.479 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_002108.4_HLA-C) Pr(w>1) post mean +- SE for w 48 S 0.898 8.060 +- 2.808 97 A 0.989* 8.782 +- 1.631 104 N 0.669 6.157 +- 4.030 121 R 0.997** 8.849 +- 1.456 138 D 0.980* 8.706 +- 1.789 140 S 0.938 8.366 +- 2.382 171 L 0.723 6.590 +- 3.851 180 L 0.993** 8.815 +- 1.548 187 T 0.996** 8.838 +- 1.485 208 P 0.542 5.065 +- 4.181 329 A 0.867 7.800 +- 3.074 362 T 0.868 7.807 +- 3.066