--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Nov 24 19:49:58 WET 2016 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=CLUSTALW2 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/ADOPS/320/Ncc69-PA/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/320/Ncc69-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/320/Ncc69-PA/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/320/Ncc69-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -13668.72 -13684.09 2 -13668.66 -13685.13 -------------------------------------- TOTAL -13668.69 -13684.74 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/320/Ncc69-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/320/Ncc69-PA/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/320/Ncc69-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.237634 0.002669 1.140422 1.340656 1.235454 1409.20 1412.70 1.000 r(A<->C){all} 0.109507 0.000097 0.088605 0.127410 0.109276 790.70 901.12 1.000 r(A<->G){all} 0.223343 0.000209 0.196661 0.252694 0.223032 800.28 841.66 1.001 r(A<->T){all} 0.110672 0.000141 0.087439 0.133340 0.110287 1001.56 1019.13 1.000 r(C<->G){all} 0.082871 0.000049 0.069883 0.097141 0.082590 1251.88 1258.76 1.000 r(C<->T){all} 0.416121 0.000298 0.383444 0.450815 0.416032 788.22 809.47 1.000 r(G<->T){all} 0.057486 0.000049 0.045054 0.072224 0.057178 1053.93 1079.17 1.000 pi(A){all} 0.210599 0.000043 0.198463 0.223696 0.210690 752.53 811.29 1.000 pi(C){all} 0.283885 0.000045 0.271276 0.297623 0.283927 981.80 1005.58 1.000 pi(G){all} 0.286076 0.000052 0.271879 0.300178 0.286004 1152.20 1156.27 1.000 pi(T){all} 0.219440 0.000039 0.208077 0.232544 0.219455 902.81 959.12 1.000 alpha{1,2} 0.147207 0.000071 0.130573 0.163676 0.146725 1124.91 1205.27 1.000 alpha{3} 4.661658 0.869327 3.068049 6.505394 4.529564 1201.39 1281.58 1.000 pinvar{all} 0.351462 0.000459 0.308482 0.390695 0.352034 1278.79 1311.21 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 -12686.009811 Model 2: PositiveSelection -12686.009814 Model 0: one-ratio -12857.308482 Model 3: discrete -12638.132263 Model 7: beta -12656.265365 Model 8: beta&w>1 -12639.811991 Model 0 vs 1 342.59734200000094 Model 2 vs 1 5.999998393235728E-6 Model 8 vs 7 32.906747999997606 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_Ncc69-PA) Pr(w>1) post mean +- SE for w 35 A 0.917 1.745 38 P 0.958* 1.809 44 A 0.984* 1.852 46 A 0.828 1.603 47 G 0.658 1.331 48 A 0.982* 1.848 49 G 0.513 1.100 50 A 0.985* 1.853 52 A 1.000** 1.877 388 A 0.833 1.611 449 Q 0.855 1.647 487 S 0.771 1.512 861 V 0.826 1.599 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: D_melanogaster_Ncc69-PA) Pr(w>1) post mean +- SE for w 35 A 0.875 1.413 +- 0.323 38 P 0.931 1.464 +- 0.273 44 A 0.948 1.480 +- 0.242 46 A 0.851 1.385 +- 0.364 47 G 0.778 1.303 +- 0.443 48 A 0.950* 1.482 +- 0.241 49 G 0.705 1.223 +- 0.488 50 A 0.954* 1.485 +- 0.235 52 A 0.994** 1.519 +- 0.163 388 A 0.839 1.376 +- 0.364 449 Q 0.865 1.400 +- 0.350 487 S 0.821 1.355 +- 0.392 489 V 0.660 1.186 +- 0.483 505 N 0.559 1.079 +- 0.506 861 V 0.834 1.371 +- 0.369