--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 21:27:29 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-DPB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/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 -4411.57 -4439.47 2 -4412.00 -4437.69 -------------------------------------- TOTAL -4411.76 -4438.94 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DPB1/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} 1.311948 0.007611 1.153000 1.496000 1.307000 1.000 r(A<->C){all} 0.095493 0.000219 0.068544 0.126381 0.094675 1.000 r(A<->G){all} 0.251606 0.000629 0.204519 0.302783 0.250939 1.000 r(A<->T){all} 0.131658 0.000404 0.094393 0.173911 0.130884 1.002 r(C<->G){all} 0.088068 0.000142 0.066288 0.113269 0.087352 1.001 r(C<->T){all} 0.352732 0.000880 0.295231 0.410377 0.352657 1.000 r(G<->T){all} 0.080443 0.000174 0.056402 0.108313 0.079709 1.001 pi(A){all} 0.225367 0.000179 0.199610 0.252287 0.225029 1.000 pi(C){all} 0.274419 0.000199 0.247549 0.302189 0.274053 1.000 pi(G){all} 0.317525 0.000211 0.289375 0.346309 0.317246 1.000 pi(T){all} 0.182689 0.000147 0.159618 0.207011 0.182315 1.000 alpha{1,2} 0.401000 0.005573 0.282508 0.577192 0.391201 1.000 alpha{3} 4.420312 207.782930 1.028336 16.983666 2.132486 1.004 pinvar{all} 0.234107 0.003978 0.100442 0.346728 0.237641 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 -4296.78762 Model 7: beta -4339.577445 Model 1: NearlyNeutral -4331.797585 Model 2: PositiveSelection -4297.35627 Model 2 vs 1 68.88263000000006 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_002112.3_HLA-DPB1) Pr(w>1) post mean +- SE for w 10 R 0.760 3.586 24 S 0.531 2.809 37 F 0.658 3.239 39 G 1.000** 4.405 41 Q 0.984* 4.349 63 F 0.902 4.071 83 A 1.000** 4.404 90 I 1.000** 4.405 93 E 0.952* 4.240 254 A 0.976* 4.323 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_002112.3_HLA-DPB1) Pr(w>1) post mean +- SE for w 10 R 0.704 3.190 +- 1.556 24 S 0.567 2.839 +- 1.768 37 F 0.640 2.973 +- 1.600 39 G 1.000** 4.552 +- 1.223 41 Q 0.976* 4.431 +- 1.271 63 F 0.848 3.796 +- 1.455 83 A 1.000** 4.551 +- 1.224 90 I 1.000** 4.552 +- 1.223 93 E 0.915 4.107 +- 1.358 254 A 0.975* 4.449 +- 1.310 Model 8 vs 7 85.57964999999967 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_002112.3_HLA-DPB1) Pr(w>1) post mean +- SE for w 7 A 0.658 2.290 8 A 0.899 2.849 10 R 0.990* 3.055 15 T 0.745 2.498 24 S 0.866 2.766 36 L 0.935 2.931 37 F 0.978* 3.029 39 G 1.000** 3.078 41 Q 0.999** 3.075 46 F 0.705 2.387 52 F 0.531 1.995 63 F 0.995** 3.067 64 A 0.890 2.829 83 A 1.000** 3.078 90 I 1.000** 3.078 93 E 0.998** 3.073 94 K 0.897 2.844 97 V 0.805 2.634 117 R 0.667 2.287 254 A 0.996** 3.069 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_002112.3_HLA-DPB1) Pr(w>1) post mean +- SE for w 8 A 0.678 2.535 +- 1.239 10 R 0.955* 3.371 +- 0.829 24 S 0.771 2.847 +- 1.251 36 L 0.793 2.882 +- 1.163 37 F 0.921 3.267 +- 0.932 39 G 1.000** 3.511 +- 0.664 41 Q 0.996** 3.501 +- 0.681 46 F 0.520 2.100 +- 1.322 63 F 0.982* 3.456 +- 0.739 64 A 0.712 2.652 +- 1.248 83 A 1.000** 3.511 +- 0.665 90 I 1.000** 3.511 +- 0.664 93 E 0.991** 3.485 +- 0.701 94 K 0.677 2.536 +- 1.242 97 V 0.541 2.151 +- 1.257 117 R 0.520 2.105 +- 1.364 254 A 0.992** 3.489 +- 0.702