--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Nov 24 20:49:31 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-PC/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/320/Ncc69-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/320/Ncc69-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/320/Ncc69-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -13823.70 -13839.66 2 -13822.98 -13839.00 -------------------------------------- TOTAL -13823.28 -13839.38 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/320/Ncc69-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/320/Ncc69-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/320/Ncc69-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} 1.214959 0.002486 1.120996 1.312710 1.214481 1322.28 1348.94 1.000 r(A<->C){all} 0.108445 0.000101 0.089141 0.128172 0.107962 1020.99 1069.59 1.001 r(A<->G){all} 0.222412 0.000211 0.195315 0.250540 0.222439 802.18 868.44 1.000 r(A<->T){all} 0.111026 0.000138 0.089320 0.134261 0.110609 906.40 1031.49 1.000 r(C<->G){all} 0.083203 0.000048 0.069883 0.097102 0.082936 914.41 1017.00 1.000 r(C<->T){all} 0.417196 0.000308 0.382144 0.449443 0.417103 692.28 749.67 1.000 r(G<->T){all} 0.057718 0.000046 0.045084 0.071748 0.057401 1151.39 1160.80 1.000 pi(A){all} 0.213314 0.000042 0.200897 0.226007 0.213223 822.89 846.30 1.000 pi(C){all} 0.283460 0.000048 0.270387 0.296953 0.283426 911.40 930.11 1.000 pi(G){all} 0.285503 0.000051 0.271945 0.299224 0.285564 966.71 986.99 1.000 pi(T){all} 0.217723 0.000038 0.205549 0.229240 0.217595 803.37 865.94 1.000 alpha{1,2} 0.149511 0.000069 0.132493 0.165355 0.149458 1283.08 1346.98 1.000 alpha{3} 4.618395 0.823988 3.029605 6.510589 4.514315 1197.23 1331.23 1.000 pinvar{all} 0.358943 0.000459 0.316354 0.398869 0.358808 1246.31 1249.55 1.001 ------------------------------------------------------------------------------------------------------ * 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 -12837.484247 Model 2: PositiveSelection -12837.484256 Model 0: one-ratio -13006.984516 Model 3: discrete -12792.236775 Model 7: beta -12810.637666 Model 8: beta&w>1 -12793.530163 Model 0 vs 1 339.00053800000023 Model 2 vs 1 1.799999881768599E-5 Model 8 vs 7 34.21500600000218 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-PC) Pr(w>1) post mean +- SE for w 35 A 0.929 1.765 38 P 0.961* 1.817 44 A 0.986* 1.857 46 A 0.843 1.627 47 G 0.665 1.343 48 A 0.983* 1.852 49 G 0.521 1.112 50 A 0.986* 1.856 52 A 1.000** 1.879 388 A 0.850 1.639 449 Q 0.858 1.651 487 S 0.785 1.535 861 V 0.845 1.631 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-PC) Pr(w>1) post mean +- SE for w 35 A 0.880 1.417 +- 0.317 38 P 0.932 1.464 +- 0.271 44 A 0.949 1.481 +- 0.240 46 A 0.854 1.388 +- 0.361 47 G 0.777 1.302 +- 0.443 48 A 0.951* 1.482 +- 0.240 49 G 0.704 1.223 +- 0.488 50 A 0.954* 1.485 +- 0.234 52 A 0.994** 1.519 +- 0.162 388 A 0.844 1.380 +- 0.360 449 Q 0.863 1.397 +- 0.353 487 S 0.824 1.358 +- 0.390 489 V 0.666 1.192 +- 0.480 505 N 0.568 1.089 +- 0.504 861 V 0.840 1.377 +- 0.364