--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Fri Nov 03 12:07:39 WET 2017 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= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/Srevisao1/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S7_17Malus/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/ADOPS1/Srevisao1/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -7915.22 -7935.70 2 -7915.01 -7933.70 -------------------------------------- TOTAL -7915.11 -7935.13 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/Srevisao1/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S7_17Malus/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/ADOPS1/Srevisao1/S7_17Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.589672 0.004085 1.456892 1.705429 1.587433 1043.54 1272.27 1.000 r(A<->C){all} 0.117515 0.000130 0.096695 0.141061 0.117128 988.54 1065.17 1.000 r(A<->G){all} 0.303197 0.000325 0.269052 0.338053 0.302873 817.32 896.92 1.001 r(A<->T){all} 0.074985 0.000054 0.060870 0.089325 0.074626 812.45 1005.82 1.000 r(C<->G){all} 0.154773 0.000220 0.126708 0.184607 0.154099 639.35 895.64 1.000 r(C<->T){all} 0.261598 0.000287 0.226693 0.292429 0.260863 807.44 934.66 1.001 r(G<->T){all} 0.087932 0.000083 0.070630 0.105576 0.087740 1040.30 1081.95 1.000 pi(A){all} 0.300437 0.000122 0.280056 0.322574 0.300170 1009.77 1072.74 1.000 pi(C){all} 0.171786 0.000076 0.155331 0.188508 0.171553 823.94 959.45 1.000 pi(G){all} 0.190639 0.000084 0.172114 0.207917 0.190579 1008.26 1052.83 1.000 pi(T){all} 0.337137 0.000135 0.315026 0.360121 0.337238 938.56 1017.40 1.000 alpha{1,2} 0.839014 0.011414 0.645197 1.044926 0.828820 1369.33 1384.42 1.000 alpha{3} 1.893832 0.173251 1.191888 2.820625 1.837140 1252.48 1376.74 1.000 pinvar{all} 0.031848 0.000651 0.000000 0.081065 0.025492 1414.25 1436.11 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 -5328.244827 Model 2: PositiveSelection -5288.218606 Model 0: one-ratio -5473.429714 Model 3: discrete -5287.815107 Model 7: beta -5340.138853 Model 8: beta&w>1 -5289.777434 Model 0 vs 1 290.36977399999887 Model 2 vs 1 80.05244200000016 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S7_SFBB1) Pr(w>1) post mean +- SE for w 7 N 0.997** 3.596 13 R 0.999** 3.603 17 P 0.995** 3.591 46 L 0.988* 3.573 53 E 0.934 3.433 66 A 0.650 2.692 93 S 0.999** 3.601 94 R 0.925 3.409 100 I 0.999** 3.602 102 T 0.999** 3.603 131 Q 0.525 2.367 148 T 0.600 2.564 163 E 0.794 3.069 166 C 0.965* 3.513 182 T 1.000** 3.604 184 E 0.992** 3.583 232 P 0.662 2.724 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: S7_SFBB1) Pr(w>1) post mean +- SE for w 7 N 0.996** 3.657 +- 0.432 13 R 0.999** 3.668 +- 0.402 17 P 0.994** 3.653 +- 0.447 46 L 0.985* 3.629 +- 0.508 53 E 0.922 3.458 +- 0.810 66 A 0.598 2.554 +- 1.300 93 S 0.999** 3.666 +- 0.409 94 R 0.904 3.402 +- 0.862 100 I 0.999** 3.666 +- 0.407 102 T 0.999** 3.667 +- 0.403 148 T 0.552 2.436 +- 1.318 163 E 0.745 2.948 +- 1.179 166 C 0.957* 3.552 +- 0.664 182 T 1.000** 3.669 +- 0.398 184 E 0.990* 3.642 +- 0.476 232 P 0.615 2.606 +- 1.301 Model 8 vs 7 100.7228380000015 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S7_SFBB1) Pr(w>1) post mean +- SE for w 7 N 0.999** 3.050 13 R 1.000** 3.051 17 P 0.999** 3.048 46 L 0.996** 3.044 51 F 0.815 2.645 53 E 0.974* 2.995 55 G 0.730 2.452 66 A 0.881 2.790 93 S 1.000** 3.051 94 R 0.980* 3.007 100 I 1.000** 3.051 102 T 1.000** 3.051 119 Q 0.634 2.225 131 Q 0.776 2.551 134 Y 0.545 2.048 148 T 0.831 2.676 149 I 0.617 2.212 163 E 0.947 2.937 166 C 0.989* 3.028 182 T 1.000** 3.051 184 E 0.997** 3.046 212 K 0.747 2.491 232 P 0.871 2.766 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: S7_SFBB1) Pr(w>1) post mean +- SE for w 7 N 0.999** 2.852 +- 0.502 13 R 1.000** 2.854 +- 0.500 17 P 0.998** 2.851 +- 0.505 46 L 0.996** 2.845 +- 0.513 51 F 0.807 2.381 +- 0.835 53 E 0.971* 2.790 +- 0.590 55 G 0.748 2.258 +- 0.905 65 L 0.567 1.855 +- 0.942 66 A 0.869 2.537 +- 0.782 78 G 0.574 1.873 +- 0.976 93 S 1.000** 2.854 +- 0.500 94 R 0.975* 2.794 +- 0.577 100 I 1.000** 2.854 +- 0.500 102 T 1.000** 2.854 +- 0.500 119 Q 0.672 2.104 +- 0.986 131 Q 0.783 2.343 +- 0.889 134 Y 0.635 1.997 +- 0.915 148 T 0.828 2.444 +- 0.843 149 I 0.677 2.075 +- 0.882 163 E 0.932 2.688 +- 0.670 166 C 0.987* 2.825 +- 0.541 182 T 1.000** 2.855 +- 0.499 184 E 0.997** 2.848 +- 0.510 212 K 0.760 2.280 +- 0.892 232 P 0.863 2.528 +- 0.797