--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Nov 05 06:00:17 WET 2017 codeml.models=0 1 2 3 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_adops tcoffee.bin=t_coffee_ADOPS mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS1/Ebolaaminoresults/vp35/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) (Values are saved to the file /opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -5647.39 -5682.83 2 -5647.58 -5685.17 -------------------------------------- TOTAL -5647.48 -5684.57 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": Summaries are based on a total of 3002 samples from 2 runs. Each run produced 2001 samples of which 1501 samples were included. Parameter summaries saved to file "/opt/ADOPS1/Ebolaaminoresults/vp35/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 4.390524 0.106451 3.815348 5.067019 4.380022 758.61 817.83 1.000 r(A<->C){all} 0.096736 0.000227 0.067460 0.126552 0.096330 803.28 885.90 1.001 r(A<->G){all} 0.379942 0.000894 0.323439 0.436753 0.378891 711.15 727.13 1.001 r(A<->T){all} 0.065118 0.000159 0.039865 0.088824 0.064854 984.45 987.69 1.001 r(C<->G){all} 0.016982 0.000100 0.000832 0.036035 0.015748 770.05 906.22 1.001 r(C<->T){all} 0.385830 0.000898 0.326438 0.442239 0.385809 676.48 747.90 1.001 r(G<->T){all} 0.055392 0.000194 0.028628 0.082754 0.054977 799.81 802.77 1.001 pi(A){all} 0.329823 0.000111 0.309499 0.350440 0.329755 855.79 946.28 1.000 pi(C){all} 0.231115 0.000087 0.212948 0.249007 0.231157 770.61 897.13 1.001 pi(G){all} 0.200227 0.000077 0.183488 0.217448 0.200105 991.86 1010.61 1.000 pi(T){all} 0.238835 0.000091 0.220368 0.257414 0.238710 1119.16 1130.32 1.000 alpha{1,2} 0.200565 0.000255 0.171117 0.232789 0.199559 1010.29 1175.20 1.000 alpha{3} 4.284052 0.959495 2.629606 6.271498 4.174216 1180.99 1267.07 1.000 pinvar{all} 0.017900 0.000179 0.000001 0.043691 0.015084 986.04 1186.90 1.000 ------------------------------------------------------------------------------------------------------ * Convergence diagnostic (ESS = Estimated Sample Size); min and avg values correspond to minimal and average ESS among runs. ESS value below 100 may indicate that the parameter is undersampled. + Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman and Rubin, 1992) should approach 1.0 as runs converge. Setting sumt conformat to Simple --- CODEML SUMMARY Model 1: NearlyNeutral -5099.552346 Model 2: PositiveSelection -5099.552346 Model 0: one-ratio -5228.980528 Model 3: discrete -5055.113527 Model 7: beta -5055.916397 Model 8: beta&w>1 -5055.916487 Model 0 vs 1 258.8563639999993 Model 2 vs 1 0.0 Model 8 vs 7 1.8000000090978574E-4