--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 23:34:23 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-DQB2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB2/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 -2037.30 -2052.44 2 -2037.47 -2054.94 -------------------------------------- TOTAL -2037.38 -2054.32 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DQB2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DQB2/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} 0.332268 0.001951 0.261000 0.434000 0.327000 1.000 r(A<->C){all} 0.081725 0.000615 0.038843 0.135235 0.079424 1.000 r(A<->G){all} 0.261268 0.001789 0.183520 0.348225 0.259638 1.000 r(A<->T){all} 0.062053 0.000837 0.014580 0.126068 0.059100 1.001 r(C<->G){all} 0.088577 0.000548 0.047506 0.138371 0.086899 1.000 r(C<->T){all} 0.406853 0.002884 0.307226 0.515548 0.404763 1.000 r(G<->T){all} 0.099524 0.000811 0.049363 0.162299 0.097413 1.000 pi(A){all} 0.209974 0.000175 0.184454 0.236328 0.209752 1.000 pi(C){all} 0.276586 0.000207 0.248659 0.304914 0.276544 1.000 pi(G){all} 0.313088 0.000231 0.283459 0.343260 0.312841 1.000 pi(T){all} 0.200353 0.000166 0.175767 0.226280 0.200249 1.000 alpha{1,2} 93.297168 3646.579991 1.844282 194.456566 92.055876 1.001 alpha{3} 101.311825 3222.281802 8.074997 195.348397 100.635390 1.000 pinvar{all} 0.631657 0.003205 0.499569 0.721356 0.638699 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 -1946.637262 Model 7: beta -1947.424052 Model 1: NearlyNeutral -1946.963447 Model 2: PositiveSelection -1946.627808 Model 2 vs 1 0.6712780000002567 Model 8 vs 7 1.57358000000022