--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 19:13:01 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-DOA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOA/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 -2757.44 -2788.61 2 -2757.47 -2787.53 -------------------------------------- TOTAL -2757.46 -2788.21 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DOA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DOA/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} 0.602435 0.003419 0.506000 0.731000 0.596000 1.002 r(A<->C){all} 0.077075 0.000284 0.047765 0.113191 0.075897 1.000 r(A<->G){all} 0.398909 0.001585 0.322753 0.478178 0.397974 1.000 r(A<->T){all} 0.052724 0.000327 0.022508 0.092134 0.051082 1.001 r(C<->G){all} 0.056924 0.000131 0.036467 0.081281 0.056235 1.001 r(C<->T){all} 0.375131 0.001453 0.301542 0.450926 0.375077 1.000 r(G<->T){all} 0.039237 0.000139 0.019236 0.064860 0.038177 1.000 pi(A){all} 0.192156 0.000165 0.167814 0.217376 0.191923 1.000 pi(C){all} 0.318384 0.000236 0.288596 0.349123 0.318251 1.000 pi(G){all} 0.278358 0.000222 0.249301 0.308066 0.278171 1.000 pi(T){all} 0.211102 0.000180 0.185775 0.238094 0.210662 1.000 alpha{1,2} 41.555327 3477.108527 0.472556 186.526295 4.233821 1.000 alpha{3} 64.383429 3898.802620 0.998690 191.245575 43.370592 1.001 pinvar{all} 0.505866 0.007391 0.274045 0.607628 0.529107 1.001 --------------------------------------------------------------------------------------------- * 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 -2686.922273 Model 7: beta -2687.012962 Model 1: NearlyNeutral -2687.955325 Model 2: PositiveSelection -2687.955325 Model 2 vs 1 0.0 Model 8 vs 7 0.18137799999931303