--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Dec 09 15:11:08 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/442/Zasp52-PN/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PN/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/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -12569.93 -12583.13 2 -12570.15 -12585.42 -------------------------------------- TOTAL -12570.03 -12584.83 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PN/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/442/Zasp52-PN/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 0.809306 0.001671 0.730200 0.887305 0.808982 1046.78 1200.47 1.000 r(A<->C){all} 0.071754 0.000075 0.055367 0.088986 0.071352 1131.19 1190.34 1.001 r(A<->G){all} 0.254385 0.000300 0.220333 0.288574 0.253785 563.21 674.48 1.000 r(A<->T){all} 0.150031 0.000233 0.118606 0.178097 0.149559 809.74 876.75 1.000 r(C<->G){all} 0.063672 0.000048 0.050608 0.077794 0.063306 1047.57 1140.20 1.000 r(C<->T){all} 0.376616 0.000404 0.337296 0.415402 0.377288 532.41 708.35 1.000 r(G<->T){all} 0.083541 0.000122 0.061664 0.104847 0.082934 1027.81 1083.79 1.000 pi(A){all} 0.236978 0.000042 0.225081 0.249896 0.237257 1121.23 1172.40 1.000 pi(C){all} 0.331427 0.000049 0.317414 0.345170 0.331243 1119.70 1160.86 1.000 pi(G){all} 0.262576 0.000044 0.249869 0.275782 0.262611 1258.76 1312.03 1.000 pi(T){all} 0.169019 0.000029 0.157911 0.178999 0.169048 998.55 1047.69 1.000 alpha{1,2} 0.196306 0.000268 0.164473 0.226990 0.195504 1047.14 1193.71 1.000 alpha{3} 4.012545 0.877975 2.409171 5.928051 3.893311 1487.70 1492.76 1.000 pinvar{all} 0.461109 0.000584 0.415509 0.507535 0.461932 1269.98 1385.49 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 -10684.142614 Model 2: PositiveSelection -10679.941495 Model 0: one-ratio -10859.188842 Model 3: discrete -10669.428685 Model 7: beta -10676.944448 Model 8: beta&w>1 -10669.85157 Model 0 vs 1 350.0924559999985 Model 2 vs 1 8.402238000002399 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_Zasp52-PN) Pr(w>1) post mean +- SE for w 939 S 0.994** 8.775 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_Zasp52-PN) Pr(w>1) post mean +- SE for w 254 S 0.511 1.240 +- 0.293 256 T 0.534 1.253 +- 0.289 262 T 0.795 1.397 +- 0.202 386 T 0.565 1.281 +- 0.252 583 N 0.579 1.282 +- 0.269 747 A 0.684 1.342 +- 0.233 830 A 0.661 1.327 +- 0.248 831 T 0.588 1.287 +- 0.268 832 V 0.530 1.193 +- 0.404 834 A 0.510 1.239 +- 0.292 836 T 0.521 1.244 +- 0.295 870 F 0.695 1.347 +- 0.231 884 A 0.648 1.320 +- 0.251 920 I 0.648 1.324 +- 0.240 925 L 0.513 1.242 +- 0.290 939 S 0.934 1.467 +- 0.125 943 K 0.558 1.270 +- 0.276 945 T 0.603 1.296 +- 0.263 948 F 0.542 1.261 +- 0.277 990 P 0.503 1.161 +- 0.432 993 G 0.745 1.373 +- 0.219 Model 8 vs 7 14.185755999998946 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_Zasp52-PN) Pr(w>1) post mean +- SE for w 262 T 0.767 5.616 939 S 1.000** 7.128 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_Zasp52-PN) Pr(w>1) post mean +- SE for w 251 P 0.553 1.003 +- 0.578 254 S 0.645 1.145 +- 0.497 256 T 0.680 1.181 +- 0.482 262 T 0.967* 1.473 +- 0.150 386 T 0.773 1.289 +- 0.400 451 S 0.584 1.079 +- 0.519 460 R 0.506 0.946 +- 0.588 583 N 0.760 1.268 +- 0.427 626 G 0.514 0.954 +- 0.588 737 S 0.513 0.954 +- 0.587 738 K 0.587 1.085 +- 0.514 747 A 0.919 1.432 +- 0.235 825 I 0.575 1.029 +- 0.571 830 A 0.864 1.373 +- 0.329 831 T 0.773 1.281 +- 0.418 832 V 0.645 1.113 +- 0.542 834 A 0.644 1.144 +- 0.497 836 T 0.650 1.147 +- 0.498 870 F 0.913 1.424 +- 0.252 880 A 0.548 0.996 +- 0.579 882 A 0.554 1.006 +- 0.575 884 A 0.850 1.359 +- 0.346 886 A 0.576 1.031 +- 0.571 920 I 0.874 1.388 +- 0.304 925 L 0.651 1.152 +- 0.493 939 S 0.997** 1.498 +- 0.041 943 K 0.728 1.234 +- 0.451 945 T 0.796 1.305 +- 0.399 947 P 0.540 0.987 +- 0.581 948 F 0.709 1.216 +- 0.459 990 P 0.601 1.060 +- 0.563 993 G 0.943 1.452 +- 0.202