--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Feb 15 20:23:10 WET 2016 codeml.models= mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE tcoffee.params= tcoffee.maxSeqs=0 codeml.bin=codeml mrbayes.tburnin=2500 codeml.dir=/usr/bin/ input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/Z_B1/Zika-NS3_4/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_4/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/ADOPS/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -4928.76 -4983.65 2 -4925.80 -4999.16 -------------------------------------- TOTAL -4926.45 -4998.46 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Z_B1/Zika-NS3_4/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/ADOPS/Z_B1/Zika-NS3_4/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.901506 0.006976 0.752029 1.075270 0.896525 350.50 411.29 1.000 r(A<->C){all} 0.026667 0.000047 0.014383 0.040585 0.025990 792.07 862.28 1.000 r(A<->G){all} 0.214110 0.000951 0.157108 0.277052 0.211810 474.31 508.75 1.000 r(A<->T){all} 0.020039 0.000055 0.007348 0.034381 0.019252 801.43 809.91 1.000 r(C<->G){all} 0.006180 0.000011 0.000659 0.012935 0.005567 923.77 935.64 1.000 r(C<->T){all} 0.703350 0.001240 0.629551 0.767336 0.704535 426.95 491.19 1.000 r(G<->T){all} 0.029654 0.000068 0.014148 0.045121 0.028958 484.19 620.85 1.001 pi(A){all} 0.281612 0.000095 0.261988 0.299898 0.281564 1039.31 1155.62 1.002 pi(C){all} 0.235732 0.000078 0.219037 0.253901 0.235384 989.04 1113.83 1.001 pi(G){all} 0.278121 0.000096 0.258271 0.296422 0.278118 1133.19 1194.60 1.000 pi(T){all} 0.204535 0.000069 0.188173 0.220951 0.204203 1026.54 1074.38 1.001 alpha{1,2} 0.054845 0.000606 0.002839 0.088994 0.061138 801.42 939.36 1.000 alpha{3} 4.446388 1.165671 2.519597 6.601797 4.328784 1288.67 1292.96 1.000 pinvar{all} 0.364347 0.001165 0.300813 0.432202 0.364895 1046.36 1100.80 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: One dN/dS ratio for branches, -4658.632923