--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Nov 05 02:01:55 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/vp24/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp24/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/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -3891.89 -3922.79 2 -3891.51 -3919.53 -------------------------------------- TOTAL -3891.68 -3922.13 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp24/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/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 4.054835 0.105412 3.454792 4.714971 4.038131 961.18 1019.30 1.000 r(A<->C){all} 0.133750 0.000377 0.096895 0.171654 0.133364 841.57 888.40 1.000 r(A<->G){all} 0.304961 0.000907 0.243142 0.361515 0.304498 789.35 845.13 1.000 r(A<->T){all} 0.046135 0.000168 0.022236 0.071692 0.045258 1044.70 1047.72 1.000 r(C<->G){all} 0.017873 0.000108 0.000463 0.037294 0.016303 750.80 906.75 1.000 r(C<->T){all} 0.440652 0.001157 0.377534 0.507445 0.440138 741.63 785.49 1.000 r(G<->T){all} 0.056629 0.000194 0.031199 0.084487 0.055954 1067.58 1099.13 1.000 pi(A){all} 0.291027 0.000160 0.265597 0.314791 0.290737 1064.26 1089.46 1.000 pi(C){all} 0.230445 0.000118 0.209504 0.252417 0.230240 857.74 1009.58 1.000 pi(G){all} 0.207558 0.000128 0.185192 0.228653 0.207540 666.61 915.96 1.000 pi(T){all} 0.270970 0.000149 0.245140 0.293228 0.270866 1006.38 1116.96 1.000 alpha{1,2} 0.165518 0.000209 0.139985 0.196007 0.164526 1144.95 1268.60 1.000 alpha{3} 4.252383 1.069604 2.389553 6.254538 4.120725 1329.98 1404.12 1.000 pinvar{all} 0.037214 0.000535 0.000036 0.079521 0.034796 1314.97 1407.98 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 -3566.059905 Model 2: PositiveSelection -3566.059905 Model 0: one-ratio -3589.271015 Model 3: discrete -3544.960047 Model 7: beta -3547.782422 Model 8: beta&w>1 -3545.823393 Model 0 vs 1 46.42221999999947 Model 2 vs 1 0.0 Model 8 vs 7 3.918058000000201