--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Dec 10 21:27:39 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/443/zip-PH/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/443/zip-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/443/zip-PH/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/443/zip-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -19380.07 -19399.32 2 -19380.42 -19400.77 -------------------------------------- TOTAL -19380.23 -19400.28 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/443/zip-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/443/zip-PH/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/443/zip-PH/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.211332 0.001611 1.134579 1.293458 1.211003 1305.65 1403.33 1.001 r(A<->C){all} 0.058158 0.000030 0.047931 0.069094 0.058104 778.41 981.08 1.000 r(A<->G){all} 0.285992 0.000172 0.260138 0.310712 0.286199 719.75 802.29 1.003 r(A<->T){all} 0.096730 0.000099 0.077700 0.115973 0.096287 712.68 783.17 1.000 r(C<->G){all} 0.026110 0.000008 0.020500 0.031592 0.026004 1213.40 1224.89 1.000 r(C<->T){all} 0.484404 0.000248 0.453377 0.515234 0.484341 675.31 792.00 1.002 r(G<->T){all} 0.048606 0.000031 0.037397 0.059052 0.048440 925.63 1024.82 1.000 pi(A){all} 0.268829 0.000029 0.257974 0.279492 0.268718 978.59 1003.26 1.001 pi(C){all} 0.261372 0.000028 0.250532 0.271390 0.261320 1078.29 1078.74 1.002 pi(G){all} 0.302611 0.000031 0.291892 0.313876 0.302575 996.22 1111.90 1.000 pi(T){all} 0.167187 0.000019 0.158433 0.175262 0.167295 949.06 987.42 1.000 alpha{1,2} 0.087132 0.000015 0.079617 0.094439 0.087022 1077.19 1244.14 1.000 alpha{3} 8.214051 1.845854 5.744881 10.986490 8.080991 1410.56 1425.00 1.000 pinvar{all} 0.397966 0.000203 0.371680 0.426845 0.397790 1305.93 1333.21 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 -17880.438935 Model 2: PositiveSelection -17800.501434 Model 0: one-ratio -17826.577534 Model 3: discrete -17784.39425 Model 7: beta -17793.513361 Model 8: beta&w>1 -17791.303047 Model 0 vs 1 107.72280199999659 Model 2 vs 1 159.8750019999934 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis 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_zip-PH) Pr(w>1) post mean +- SE for w Model 8 vs 7 4.4206279999998515