--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Jan 23 17:03:42 GMT 2020 codeml.models=0 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=/usr/bin/ input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir=/opt/mrbayes_3.2.2/src tcoffee.dir= tcoffee.minScore=3 input.fasta=/data/4res/ML0283/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/4res/ML0283/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 /data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -1119.97 -1125.34 2 -1119.82 -1125.49 -------------------------------------- TOTAL -1119.89 -1125.42 -------------------------------------- Model parameter summaries over the runs sampled in files "/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/4res/ML0283/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 "/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.861028 0.088522 0.290796 1.408786 0.829430 1501.00 1501.00 1.001 r(A<->C){all} 0.161649 0.020867 0.000032 0.458766 0.119957 143.33 192.71 1.003 r(A<->G){all} 0.230111 0.027794 0.000125 0.544075 0.199065 181.79 221.10 1.019 r(A<->T){all} 0.134121 0.014486 0.000315 0.380402 0.100733 249.46 309.45 1.000 r(C<->G){all} 0.154125 0.018934 0.000009 0.426339 0.115357 203.50 220.00 1.002 r(C<->T){all} 0.206309 0.023214 0.000149 0.507305 0.174665 156.74 187.90 1.000 r(G<->T){all} 0.113685 0.012391 0.000001 0.336751 0.078620 290.49 319.40 1.000 pi(A){all} 0.181391 0.000180 0.154571 0.206759 0.181140 1389.47 1428.90 1.000 pi(C){all} 0.302359 0.000263 0.273229 0.334548 0.302019 1134.84 1238.70 1.000 pi(G){all} 0.304822 0.000258 0.275305 0.336870 0.304705 1171.70 1325.12 1.000 pi(T){all} 0.211428 0.000200 0.185141 0.240102 0.211206 1246.94 1373.97 1.000 alpha{1,2} 0.244988 0.062526 0.027341 0.675257 0.171063 1327.81 1414.40 1.001 alpha{3} 0.353939 0.217451 0.000208 1.306860 0.173479 1182.29 1267.20 1.000 pinvar{all} 0.993301 0.000020 0.984550 0.999548 0.994380 1275.83 1358.55 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 -1082.911034 Model 2: PositiveSelection -1078.17697 Model 0: one-ratio -1081.848756 Model 7: beta -1082.911006 Model 8: beta&w>1 -1080.169782 Model 0 vs 1 2.1245559999997568 Model 2 vs 1 9.468127999999979 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: NC_011896_1_WP_012634412_1_293_MLBR_RS01430) Pr(w>1) post mean +- SE for w 153 P 1.000** 999.000 174 A 1.000** 999.000 Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: NC_011896_1_WP_012634412_1_293_MLBR_RS01430) Pr(w>1) post mean +- SE for w 153 P 0.870 7.292 +- 3.128 174 A 0.975* 8.038 +- 2.332 Model 8 vs 7 5.482448000000204