--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 11 00:23:15 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/186/CG7766-PI/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/186/CG7766-PI/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/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -11539.43 -11554.18 2 -11539.66 -11555.75 -------------------------------------- TOTAL -11539.54 -11555.25 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/186/CG7766-PI/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/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.067379 0.002614 0.966162 1.163345 1.065976 1254.09 1275.43 1.000 r(A<->C){all} 0.068732 0.000079 0.051549 0.085469 0.068382 952.67 1002.10 1.000 r(A<->G){all} 0.264734 0.000346 0.228525 0.300109 0.264395 808.69 895.02 1.001 r(A<->T){all} 0.081366 0.000223 0.052348 0.109316 0.080950 892.00 918.53 1.000 r(C<->G){all} 0.083404 0.000053 0.070788 0.099021 0.083396 911.27 1056.27 1.000 r(C<->T){all} 0.447695 0.000474 0.406903 0.489943 0.447763 741.45 796.60 1.001 r(G<->T){all} 0.054068 0.000073 0.038209 0.071405 0.053799 1023.34 1189.11 1.000 pi(A){all} 0.204385 0.000041 0.191904 0.216717 0.204396 966.66 986.85 1.001 pi(C){all} 0.314901 0.000048 0.301670 0.327894 0.314933 1122.40 1172.96 1.000 pi(G){all} 0.297791 0.000051 0.283613 0.311697 0.297620 1174.71 1218.66 1.000 pi(T){all} 0.182923 0.000035 0.172221 0.195143 0.182778 987.58 1118.99 1.000 alpha{1,2} 0.090361 0.000032 0.079550 0.101712 0.090096 1122.64 1221.85 1.000 alpha{3} 5.252143 1.120007 3.450028 7.374641 5.146481 1501.00 1501.00 1.000 pinvar{all} 0.464053 0.000328 0.429534 0.499126 0.464710 1089.45 1130.10 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 -10459.356263 Model 2: PositiveSelection -10459.356296 Model 0: one-ratio -10499.099989 Model 3: discrete -10455.540937 Model 7: beta -10471.433477 Model 8: beta&w>1 -10458.925832 Model 0 vs 1 79.48745200000121 Model 2 vs 1 6.600000051548705E-5 Model 8 vs 7 25.015289999999368 Additional information for M7 vs M8: 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_CG7766-PI) Pr(w>1) post mean +- SE for w