--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Dec 02 21:43:58 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/96/CG18304-PC/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/96/CG18304-PC/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/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -22674.84 -22691.88 2 -22675.05 -22692.12 -------------------------------------- TOTAL -22674.94 -22692.01 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/96/CG18304-PC/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/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.378362 0.001783 1.290439 1.457044 1.376656 1235.10 1368.05 1.000 r(A<->C){all} 0.087775 0.000038 0.075997 0.099652 0.087709 663.76 686.03 1.000 r(A<->G){all} 0.246503 0.000116 0.225354 0.267568 0.246621 798.18 855.01 1.000 r(A<->T){all} 0.144655 0.000113 0.125112 0.167140 0.144525 827.04 860.73 1.000 r(C<->G){all} 0.053813 0.000017 0.046109 0.062053 0.053715 1091.83 1139.29 1.000 r(C<->T){all} 0.392110 0.000191 0.366214 0.418865 0.392153 763.73 781.07 1.000 r(G<->T){all} 0.075145 0.000045 0.063069 0.088790 0.074932 875.30 958.96 1.000 pi(A){all} 0.273351 0.000032 0.263216 0.285246 0.273392 768.25 896.44 1.000 pi(C){all} 0.270967 0.000029 0.260474 0.281282 0.270728 866.50 969.68 1.000 pi(G){all} 0.297671 0.000032 0.287441 0.309208 0.297606 909.31 960.24 1.000 pi(T){all} 0.158011 0.000019 0.149258 0.166010 0.157955 560.60 719.01 1.000 alpha{1,2} 0.153716 0.000044 0.141233 0.166938 0.153573 1212.70 1325.04 1.000 alpha{3} 5.058830 0.710990 3.582431 6.711710 4.970144 1285.73 1339.59 1.000 pinvar{all} 0.305418 0.000279 0.273403 0.339705 0.305716 1323.45 1346.14 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 -20645.365115 Model 2: PositiveSelection -20645.365115 Model 0: one-ratio -20914.180362 Model 3: discrete -20570.698627 Model 7: beta -20577.320931 Model 8: beta&w>1 -20570.437721 Model 0 vs 1 537.6304939999973 Model 2 vs 1 0.0 Model 8 vs 7 13.766419999999925 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_CG18304-PC) Pr(w>1) post mean +- SE for w 117 S 0.584 0.806 287 S 0.573 0.796 289 A 0.980* 1.145 290 S 0.943 1.113 303 I 0.930 1.102 306 T 0.961* 1.129 307 A 0.879 1.058 309 A 0.648 0.860 312 S 0.888 1.066 890 S 0.749 0.947 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_CG18304-PC) Pr(w>1) post mean +- SE for w 78 A 0.650 1.151 +- 0.493 117 S 0.743 1.261 +- 0.418 149 I 0.731 1.237 +- 0.447 214 P 0.586 1.081 +- 0.518 215 T 0.533 1.023 +- 0.532 234 L 0.672 1.189 +- 0.459 274 V 0.555 1.068 +- 0.500 287 S 0.733 1.251 +- 0.425 289 A 0.973* 1.479 +- 0.129 290 S 0.923 1.437 +- 0.223 301 A 0.507 0.994 +- 0.536 303 I 0.947 1.456 +- 0.190 306 T 0.935 1.448 +- 0.203 307 A 0.874 1.394 +- 0.287 309 A 0.795 1.311 +- 0.381 312 S 0.924 1.435 +- 0.231 591 L 0.560 1.076 +- 0.497 849 G 0.650 1.157 +- 0.484 890 S 0.818 1.338 +- 0.351 908 A 0.522 1.031 +- 0.509 1020 A 0.553 1.068 +- 0.498