--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Dec 04 15:59:01 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/351/Pkn-PL/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/351/Pkn-PL/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/351/Pkn-PL/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/351/Pkn-PL/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -13707.08 -13724.16 2 -13706.38 -13726.17 -------------------------------------- TOTAL -13706.67 -13725.60 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/351/Pkn-PL/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/351/Pkn-PL/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/351/Pkn-PL/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.089826 0.001927 1.003344 1.173536 1.088659 915.96 1173.85 1.000 r(A<->C){all} 0.099591 0.000075 0.083574 0.117535 0.099336 692.74 965.26 1.000 r(A<->G){all} 0.290982 0.000238 0.259673 0.319223 0.291222 599.03 733.80 1.000 r(A<->T){all} 0.100159 0.000121 0.079103 0.121904 0.099814 896.06 1003.56 1.000 r(C<->G){all} 0.050952 0.000027 0.040632 0.060950 0.050816 1175.26 1281.52 1.000 r(C<->T){all} 0.397551 0.000307 0.364850 0.433190 0.397469 752.65 771.76 1.000 r(G<->T){all} 0.060764 0.000051 0.047334 0.075001 0.060332 1142.06 1152.89 1.001 pi(A){all} 0.228520 0.000040 0.215386 0.240037 0.228476 781.41 925.25 1.000 pi(C){all} 0.277916 0.000043 0.263726 0.289856 0.278098 991.75 1033.83 1.000 pi(G){all} 0.297166 0.000047 0.283859 0.310336 0.297065 830.96 941.72 1.000 pi(T){all} 0.196398 0.000032 0.185586 0.207872 0.196417 1031.72 1149.85 1.000 alpha{1,2} 0.123053 0.000043 0.111042 0.136493 0.122698 1050.19 1260.93 1.000 alpha{3} 6.477441 1.458093 4.329649 8.873616 6.359523 1323.63 1330.72 1.000 pinvar{all} 0.377676 0.000376 0.339054 0.415667 0.377809 1206.41 1215.06 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 -12679.576314 Model 2: PositiveSelection -12676.328543 Model 0: one-ratio -12805.798265 Model 3: discrete -12672.776531 Model 7: beta -12680.258515 Model 8: beta&w>1 -12669.264961 Model 0 vs 1 252.44390199999907 Model 2 vs 1 6.495542000000569 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: D_melanogaster_Pkn-PL) Pr(w>1) post mean +- SE for w 785 A 0.986* 5.176 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_Pkn-PL) Pr(w>1) post mean +- SE for w 162 A 0.663 1.335 +- 0.250 372 I 0.643 1.319 +- 0.268 598 L 0.527 1.264 +- 0.259 784 S 0.695 1.352 +- 0.245 785 A 0.955* 1.483 +- 0.136 957 R 0.553 1.244 +- 0.343 Model 8 vs 7 21.987107999997534 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_Pkn-PL) Pr(w>1) post mean +- SE for w 784 S 0.527 2.026 785 A 1.000** 3.543 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_Pkn-PL) Pr(w>1) post mean +- SE for w 155 N 0.565 1.081 +- 0.496 162 A 0.893 1.407 +- 0.283 372 I 0.836 1.344 +- 0.369 598 L 0.745 1.264 +- 0.418 708 S 0.552 1.043 +- 0.529 734 T 0.622 1.120 +- 0.508 774 S 0.529 0.974 +- 0.585 784 S 0.918 1.430 +- 0.249 785 A 0.998** 1.500 +- 0.048 824 S 0.538 1.053 +- 0.502 957 R 0.713 1.204 +- 0.487