--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 20:01:36 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-DOB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOB/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 -3314.80 -3342.00 2 -3314.49 -3342.64 -------------------------------------- TOTAL -3314.63 -3342.37 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DOB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOB/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} 0.664970 0.002172 0.581000 0.764000 0.662000 1.005 r(A<->C){all} 0.097177 0.000324 0.064769 0.135653 0.096288 1.000 r(A<->G){all} 0.270211 0.000726 0.219817 0.326032 0.269522 1.000 r(A<->T){all} 0.048156 0.000175 0.025365 0.076837 0.047087 1.001 r(C<->G){all} 0.141512 0.000345 0.107435 0.179443 0.140725 1.000 r(C<->T){all} 0.390233 0.001013 0.329916 0.453873 0.389666 1.000 r(G<->T){all} 0.052711 0.000147 0.030822 0.078338 0.052063 1.000 pi(A){all} 0.219441 0.000158 0.195434 0.244074 0.219162 1.000 pi(C){all} 0.244527 0.000160 0.220144 0.269462 0.244371 1.000 pi(G){all} 0.288959 0.000189 0.262353 0.316546 0.289040 1.000 pi(T){all} 0.247073 0.000172 0.221702 0.273338 0.246906 1.000 alpha{1,2} 43.368315 3540.845816 0.779146 187.655306 5.397278 1.015 alpha{3} 93.193195 3581.724551 3.278866 194.536091 91.022956 1.005 pinvar{all} 0.367901 0.005195 0.197152 0.473994 0.380638 1.010 --------------------------------------------------------------------------------------------- * 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 -2704.917655 Model 7: beta -2708.679026 Model 1: NearlyNeutral -2707.138142 Model 2: PositiveSelection -2704.790433 Model 2 vs 1 4.695417999999336 Model 8 vs 7 7.522741999999198 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_002111.1_HLA-DOB) Pr(w>1) post mean +- SE for w 7 S 0.637 2.360 43 R 0.511 2.047 56 K 0.988* 3.228 67 S 0.827 2.835 232 L 0.518 2.066 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_002111.1_HLA-DOB) Pr(w>1) post mean +- SE for w 7 S 0.767 2.239 +- 1.106 43 R 0.691 2.065 +- 1.120 56 K 0.981* 2.642 +- 0.879 67 S 0.881 2.471 +- 1.010 227 S 0.620 1.931 +- 1.172 232 L 0.695 2.076 +- 1.120