--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Nov 05 07:36:45 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/vp40/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp40/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/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -6286.82 -6321.29 2 -6287.20 -6315.91 -------------------------------------- TOTAL -6286.99 -6320.61 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp40/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/vp40/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 4.047650 0.093518 3.482754 4.652256 4.038287 909.71 1119.77 1.000 r(A<->C){all} 0.123958 0.000245 0.096810 0.157824 0.123320 966.44 1038.56 1.001 r(A<->G){all} 0.385542 0.000805 0.327096 0.437811 0.385541 690.27 777.39 1.000 r(A<->T){all} 0.061770 0.000209 0.034669 0.090605 0.060942 667.14 790.18 1.000 r(C<->G){all} 0.008225 0.000049 0.000001 0.022351 0.006529 728.30 850.79 1.000 r(C<->T){all} 0.355778 0.000784 0.300188 0.408550 0.354920 932.44 934.00 1.001 r(G<->T){all} 0.064727 0.000197 0.037525 0.090991 0.064022 961.59 1007.77 1.000 pi(A){all} 0.270993 0.000077 0.252723 0.287538 0.270824 1131.15 1189.53 1.000 pi(C){all} 0.271410 0.000079 0.254947 0.290143 0.271688 1113.05 1181.10 1.000 pi(G){all} 0.226877 0.000072 0.210325 0.243526 0.226839 1208.63 1269.77 1.000 pi(T){all} 0.230720 0.000069 0.215884 0.247529 0.230548 939.66 946.95 1.000 alpha{1,2} 0.166748 0.000143 0.143714 0.189751 0.165813 938.88 1103.77 1.000 alpha{3} 3.993471 0.811470 2.358286 5.757092 3.880608 1394.17 1447.58 1.000 pinvar{all} 0.035730 0.000455 0.000016 0.073194 0.033683 1460.73 1480.86 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 -4769.53679 Model 2: PositiveSelection -4769.53679 Model 0: one-ratio -4841.668108 Model 3: discrete -4734.507062 Model 7: beta -4737.765685 Model 8: beta&w>1 -4737.766103 Model 0 vs 1 144.26263599999947 Model 2 vs 1 0.0 Model 8 vs 7 8.35999999253545E-4