--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Nov 10 18:46:50 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/191/CG8312-PA/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/191/CG8312-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/191/CG8312-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/191/CG8312-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -9105.76 -9126.01 2 -9105.91 -9125.76 -------------------------------------- TOTAL -9105.83 -9125.89 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/191/CG8312-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/191/CG8312-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/191/CG8312-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} 0.797308 0.001733 0.715572 0.877058 0.796028 1245.63 1373.32 1.000 r(A<->C){all} 0.085027 0.000102 0.065567 0.104218 0.084534 927.09 999.24 1.000 r(A<->G){all} 0.191224 0.000271 0.159482 0.223138 0.190815 748.12 809.51 1.000 r(A<->T){all} 0.106758 0.000256 0.076000 0.138981 0.106150 742.72 834.22 1.000 r(C<->G){all} 0.071431 0.000057 0.057510 0.086402 0.071185 949.61 1071.21 1.000 r(C<->T){all} 0.453254 0.000543 0.408258 0.498942 0.453114 674.83 729.80 1.000 r(G<->T){all} 0.092306 0.000137 0.071058 0.115565 0.091863 1055.36 1139.35 1.001 pi(A){all} 0.243624 0.000062 0.228348 0.259040 0.243516 1013.37 1097.30 1.000 pi(C){all} 0.298177 0.000063 0.282092 0.312819 0.298346 1030.66 1075.34 1.000 pi(G){all} 0.308598 0.000069 0.291241 0.323689 0.308632 1075.68 1105.99 1.000 pi(T){all} 0.149601 0.000038 0.137858 0.161733 0.149385 901.22 911.77 1.000 alpha{1,2} 0.164519 0.000231 0.135573 0.194509 0.164507 1279.15 1336.09 1.000 alpha{3} 4.088486 1.000038 2.261959 6.037891 3.953266 985.55 1157.79 1.003 pinvar{all} 0.326374 0.001165 0.259287 0.391647 0.328481 1079.13 1193.32 1.002 ------------------------------------------------------------------------------------------------------ * 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 -7985.933295 Model 2: PositiveSelection -7985.933295 Model 0: one-ratio -8098.578686 Model 3: discrete -7960.665157 Model 7: beta -7967.58304 Model 8: beta&w>1 -7961.029397 Model 0 vs 1 225.29078200000004 Model 2 vs 1 0.0 Model 8 vs 7 13.107286000000386 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_CG8312-PA) Pr(w>1) post mean +- SE for w 9 S 0.919 1.616 13 D 0.996** 1.723 48 V 0.752 1.383 93 A 0.924 1.624 588 T 0.767 1.406 668 A 0.940 1.646 832 T 0.596 1.168 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_CG8312-PA) Pr(w>1) post mean +- SE for w 9 S 0.933 1.447 +- 0.231 13 D 0.981* 1.490 +- 0.126 48 V 0.867 1.380 +- 0.335 52 A 0.622 1.090 +- 0.557 93 A 0.929 1.445 +- 0.232 96 T 0.681 1.183 +- 0.489 97 T 0.595 1.091 +- 0.520 98 A 0.629 1.129 +- 0.507 484 S 0.667 1.187 +- 0.463 588 T 0.853 1.376 +- 0.323 635 T 0.531 1.042 +- 0.510 668 A 0.927 1.444 +- 0.229 832 T 0.778 1.304 +- 0.387 833 S 0.728 1.214 +- 0.498