--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Nov 21 18:38:33 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/295/Lnk-PB/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/295/Lnk-PB/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/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8839.22 -8860.25 2 -8840.70 -8859.68 -------------------------------------- TOTAL -8839.71 -8860.00 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/295/Lnk-PB/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/295/Lnk-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.287773 0.004878 1.150280 1.424896 1.287110 1459.31 1480.15 1.000 r(A<->C){all} 0.106563 0.000120 0.084778 0.127458 0.106175 1015.72 1116.37 1.000 r(A<->G){all} 0.215904 0.000283 0.180668 0.247118 0.216001 874.12 900.12 1.000 r(A<->T){all} 0.125174 0.000224 0.095898 0.154783 0.124685 1106.27 1144.86 1.000 r(C<->G){all} 0.075111 0.000066 0.059770 0.091412 0.074788 943.13 1069.18 1.000 r(C<->T){all} 0.404663 0.000491 0.359532 0.445888 0.404566 744.52 772.36 1.000 r(G<->T){all} 0.072585 0.000103 0.053422 0.092756 0.072192 924.07 1039.04 1.000 pi(A){all} 0.233590 0.000068 0.218395 0.250840 0.233624 1092.26 1097.14 1.000 pi(C){all} 0.293118 0.000079 0.275755 0.310442 0.293029 920.87 987.37 1.000 pi(G){all} 0.296369 0.000084 0.279361 0.315628 0.296290 1070.01 1080.12 1.000 pi(T){all} 0.176922 0.000054 0.163066 0.191290 0.176753 812.38 895.29 1.000 alpha{1,2} 0.165352 0.000136 0.143367 0.187788 0.164705 1289.99 1330.27 1.000 alpha{3} 4.578154 0.942142 2.836384 6.571339 4.448044 1480.95 1490.98 1.000 pinvar{all} 0.367865 0.000631 0.318930 0.418231 0.367992 1258.34 1341.16 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 -7916.756018 Model 2: PositiveSelection -7916.756039 Model 0: one-ratio -7992.480109 Model 3: discrete -7907.483779 Model 7: beta -7913.023214 Model 8: beta&w>1 -7908.266947 Model 0 vs 1 151.4481820000001 Model 2 vs 1 4.199999966658652E-5 Model 8 vs 7 9.512533999999505 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_Lnk-PB) Pr(w>1) post mean +- SE for w 36 A 0.731 1.131 323 S 0.940 1.372 531 S 0.608 0.986 543 N 0.932 1.362 571 S 0.563 0.934 576 T 0.700 1.094 681 G 0.991** 1.429 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_Lnk-PB) Pr(w>1) post mean +- SE for w 36 A 0.804 1.325 +- 0.377 323 S 0.918 1.436 +- 0.245 531 S 0.770 1.282 +- 0.423 543 N 0.917 1.434 +- 0.249 571 S 0.741 1.252 +- 0.444 576 T 0.790 1.310 +- 0.390 681 G 0.972* 1.483 +- 0.150