--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Tue Nov 07 11:33:58 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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/ClustalW2/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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -8085.47 -8107.94 2 -8085.94 -8105.41 -------------------------------------- TOTAL -8085.68 -8107.32 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/ClustalW2/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/S2novarevisao/ClustalW2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.444742 0.003042 1.338398 1.552694 1.444209 1316.68 1408.84 1.000 r(A<->C){all} 0.103526 0.000113 0.081898 0.123821 0.103355 904.68 1001.19 1.000 r(A<->G){all} 0.296438 0.000310 0.262285 0.329496 0.296411 732.31 823.04 1.000 r(A<->T){all} 0.075199 0.000053 0.061327 0.090161 0.075138 934.70 983.86 1.000 r(C<->G){all} 0.150343 0.000214 0.120390 0.178529 0.150372 842.35 917.42 1.000 r(C<->T){all} 0.287041 0.000298 0.255438 0.323399 0.286469 767.04 792.46 1.000 r(G<->T){all} 0.087453 0.000080 0.069785 0.104779 0.087248 1044.11 1111.76 1.000 pi(A){all} 0.300048 0.000123 0.279477 0.322492 0.299793 860.17 862.38 1.000 pi(C){all} 0.170234 0.000075 0.152097 0.185967 0.170004 909.42 1049.36 1.000 pi(G){all} 0.190285 0.000078 0.173744 0.208339 0.190258 979.38 1049.38 1.000 pi(T){all} 0.339433 0.000136 0.316789 0.362299 0.339284 886.47 913.36 1.001 alpha{1,2} 0.890622 0.015896 0.652998 1.128527 0.872225 1108.53 1163.72 1.000 alpha{3} 1.829502 0.161855 1.087278 2.584057 1.769971 1166.58 1249.10 1.001 pinvar{all} 0.034348 0.000783 0.000046 0.091076 0.027678 1110.38 1158.99 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 -5305.117167 Model 2: PositiveSelection -5276.079396 Model 0: one-ratio -5412.424888 Model 3: discrete -5274.324693 Model 7: beta -5310.74118 Model 8: beta&w>1 -5274.669779 Model 0 vs 1 214.61544199999844 Model 2 vs 1 58.075542000000496 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S2_SFBB1) Pr(w>1) post mean +- SE for w 10 M 0.800 3.039 27 N 0.985* 3.509 33 R 0.999** 3.547 37 P 0.645 2.644 66 L 0.927 3.364 73 E 0.997** 3.540 85 L 0.745 2.899 86 A 0.541 2.379 113 R 0.887 3.260 121 I 0.999** 3.545 123 T 0.999** 3.547 140 Q 0.687 2.752 169 T 0.788 3.009 187 C 0.544 2.387 203 T 0.998** 3.545 205 E 0.961* 3.449 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: S2_SFBB1) Pr(w>1) post mean +- SE for w 10 M 0.757 3.011 +- 1.194 27 N 0.980* 3.636 +- 0.577 33 R 0.999** 3.689 +- 0.452 37 P 0.586 2.533 +- 1.322 66 L 0.909 3.438 +- 0.874 73 E 0.996** 3.682 +- 0.473 85 L 0.690 2.818 +- 1.262 113 R 0.855 3.280 +- 1.017 121 I 0.998** 3.688 +- 0.457 123 T 0.999** 3.689 +- 0.452 140 Q 0.644 2.708 +- 1.314 169 T 0.748 2.991 +- 1.210 203 T 0.998** 3.687 +- 0.459 205 E 0.951* 3.556 +- 0.720 Model 8 vs 7 72.1428020000003 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S2_SFBB1) Pr(w>1) post mean +- SE for w 10 M 0.919 2.789 27 N 0.995** 2.947 33 R 1.000** 2.956 37 P 0.854 2.652 66 L 0.972* 2.899 71 F 0.575 2.066 73 E 0.998** 2.954 75 G 0.679 2.281 85 L 0.902 2.754 86 A 0.791 2.519 113 R 0.959* 2.873 121 I 0.999** 2.956 123 T 1.000** 2.956 140 Q 0.840 2.618 152 Q 0.515 1.921 155 Y 0.588 2.095 159 A 0.512 1.932 169 T 0.906 2.760 184 E 0.643 2.209 187 C 0.781 2.496 203 T 0.999** 2.956 205 E 0.985* 2.927 255 D 0.674 2.275 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: S2_SFBB1) Pr(w>1) post mean +- SE for w 10 M 0.890 2.739 +- 0.824 27 N 0.993** 2.994 +- 0.564 33 R 1.000** 3.011 +- 0.540 37 P 0.799 2.506 +- 0.938 66 L 0.962* 2.919 +- 0.663 71 F 0.545 1.889 +- 0.990 73 E 0.998** 3.008 +- 0.545 75 G 0.627 2.087 +- 1.019 85 L 0.859 2.658 +- 0.867 86 A 0.731 2.338 +- 0.991 113 R 0.941 2.864 +- 0.716 121 I 0.999** 3.010 +- 0.541 123 T 1.000** 3.011 +- 0.540 140 Q 0.807 2.537 +- 0.953 152 Q 0.507 1.814 +- 1.036 155 Y 0.554 1.910 +- 0.989 169 T 0.878 2.711 +- 0.848 184 E 0.587 1.981 +- 0.995 187 C 0.726 2.327 +- 1.000 203 T 0.999** 3.010 +- 0.541 205 E 0.981* 2.965 +- 0.606 255 D 0.615 2.051 +- 1.004