--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Dec 07 19:27:24 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/402/Spn-PE/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PE/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/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -19698.90 -19713.21 2 -19699.20 -19713.95 -------------------------------------- TOTAL -19699.04 -19713.65 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PE/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/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.213465 0.001853 1.119721 1.288991 1.212543 1176.47 1218.16 1.000 r(A<->C){all} 0.096282 0.000059 0.081688 0.111408 0.096129 1118.36 1159.12 1.000 r(A<->G){all} 0.230257 0.000147 0.206437 0.253833 0.229974 1186.02 1187.98 1.000 r(A<->T){all} 0.137875 0.000126 0.115429 0.159439 0.137671 805.78 958.82 1.000 r(C<->G){all} 0.068004 0.000029 0.057887 0.078624 0.067981 1096.02 1101.69 1.000 r(C<->T){all} 0.397718 0.000232 0.368205 0.426746 0.397818 825.57 882.29 1.000 r(G<->T){all} 0.069864 0.000049 0.055925 0.082947 0.069802 861.36 1007.17 1.000 pi(A){all} 0.229079 0.000026 0.219368 0.239299 0.229031 1025.66 1050.86 1.000 pi(C){all} 0.305642 0.000031 0.294153 0.316267 0.305671 867.74 1031.60 1.000 pi(G){all} 0.305593 0.000033 0.293962 0.316209 0.305463 884.85 894.37 1.000 pi(T){all} 0.159686 0.000019 0.151348 0.168115 0.159607 881.00 995.50 1.000 alpha{1,2} 0.123166 0.000032 0.113050 0.135277 0.122967 1277.04 1321.00 1.000 alpha{3} 5.037804 0.792318 3.337747 6.672153 4.927351 1400.37 1413.03 1.002 pinvar{all} 0.363499 0.000293 0.330753 0.397261 0.363717 1176.05 1240.49 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 -17152.93027 Model 2: PositiveSelection -17152.930423 Model 0: one-ratio -17465.49826 Model 3: discrete -17125.27371 Model 7: beta -17137.087421 Model 8: beta&w>1 -17125.369446 Model 0 vs 1 625.1359799999991 Model 2 vs 1 3.060000017285347E-4 Model 8 vs 7 23.43594999999914 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_Spn-PE) Pr(w>1) post mean +- SE for w 56 V 0.710 0.855 143 I 0.891 1.013 149 P 0.993** 1.102 166 Q 0.976* 1.087 183 L 0.852 0.979 188 P 0.939 1.055 189 S 0.729 0.872 195 S 0.874 0.998 273 P 0.535 0.703 317 R 0.901 1.022 318 L 0.652 0.805 356 S 0.927 1.044 377 T 0.948 1.062 410 S 0.622 0.779 415 P 0.829 0.959 488 S 0.803 0.936 491 S 0.938 1.054 495 S 0.914 1.033 507 A 0.930 1.047 551 A 0.983* 1.093 564 Q 0.876 1.000 565 T 0.943 1.058 641 S 0.811 0.943 643 S 0.806 0.939 645 L 0.728 0.871 699 L 0.675 0.825 720 V 0.649 0.802 805 T 0.641 0.795 808 S 0.701 0.848 809 I 0.999** 1.107 810 Q 0.998** 1.106 956 T 0.593 0.753 1013 S 0.597 0.757 1014 S 0.996** 1.104 1016 A 0.819 0.950 1017 P 0.822 0.953 1030 H 0.594 0.755 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_Spn-PE) Pr(w>1) post mean +- SE for w 56 V 0.500 1.006 +- 0.514 143 I 0.769 1.285 +- 0.403 149 P 0.965* 1.472 +- 0.152 166 Q 0.923 1.434 +- 0.234 183 L 0.718 1.228 +- 0.448 188 P 0.857 1.371 +- 0.323 189 S 0.626 1.122 +- 0.508 195 S 0.740 1.256 +- 0.424 317 R 0.839 1.349 +- 0.355 318 L 0.523 1.010 +- 0.535 356 S 0.835 1.350 +- 0.347 377 T 0.807 1.328 +- 0.360 415 P 0.641 1.158 +- 0.472 488 S 0.710 1.215 +- 0.462 491 S 0.835 1.352 +- 0.343 495 S 0.751 1.273 +- 0.406 507 A 0.752 1.276 +- 0.400 551 A 0.887 1.404 +- 0.274 564 Q 0.656 1.181 +- 0.456 565 T 0.855 1.370 +- 0.324 641 S 0.734 1.238 +- 0.449 643 S 0.613 1.128 +- 0.484 645 L 0.520 1.028 +- 0.510 699 L 0.559 1.047 +- 0.530 805 T 0.501 0.985 +- 0.540 808 S 0.580 1.073 +- 0.522 809 I 0.989* 1.491 +- 0.082 810 Q 0.974* 1.480 +- 0.125 1014 S 0.965* 1.472 +- 0.150 1016 A 0.735 1.241 +- 0.446 1017 P 0.741 1.247 +- 0.443