--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Nov 04 00:51:58 WET 2017 codeml.models=0 1 2 3 7 8 mrbayes.mpich= mrbayes.ngen=1000000 tcoffee.alignMethod=MUSCLE 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/revmuscle/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S5/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/revmuscle/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -7424.07 -7444.15 2 -7424.04 -7441.68 -------------------------------------- TOTAL -7424.05 -7443.54 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/revmuscle/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S5/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/revmuscle/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.426375 0.003662 1.306126 1.543630 1.423657 1383.30 1414.01 1.000 r(A<->C){all} 0.107254 0.000134 0.084813 0.129427 0.107064 980.02 1043.24 1.000 r(A<->G){all} 0.323886 0.000373 0.287849 0.363455 0.323110 604.51 637.98 1.000 r(A<->T){all} 0.078767 0.000061 0.063585 0.093697 0.078639 1035.32 1037.82 1.000 r(C<->G){all} 0.138346 0.000213 0.110366 0.167488 0.137772 984.30 1054.38 1.000 r(C<->T){all} 0.270755 0.000301 0.236655 0.304718 0.270668 880.28 918.88 1.001 r(G<->T){all} 0.080992 0.000084 0.063736 0.098878 0.080549 1102.07 1132.03 1.000 pi(A){all} 0.292442 0.000112 0.271284 0.312944 0.292706 1043.16 1198.88 1.000 pi(C){all} 0.174849 0.000078 0.158255 0.192544 0.174745 980.85 1078.25 1.000 pi(G){all} 0.195289 0.000081 0.178568 0.213335 0.195274 991.53 1051.25 1.000 pi(T){all} 0.337420 0.000127 0.316082 0.359862 0.337484 1115.48 1172.99 1.000 alpha{1,2} 0.883018 0.025913 0.611356 1.205751 0.855502 935.91 1093.07 1.000 alpha{3} 1.509877 0.160454 0.867752 2.316765 1.435413 903.97 1051.19 1.000 pinvar{all} 0.060048 0.001930 0.000026 0.142941 0.051618 1027.63 1084.58 1.001 ------------------------------------------------------------------------------------------------------ * 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 -3649.488118 Model 2: PositiveSelection -3625.008556 Model 0: one-ratio -3727.832062 Model 3: discrete -3622.128473 Model 7: beta -3648.567478 Model 8: beta&w>1 -3621.601279 Model 0 vs 1 156.68788799999948 Model 2 vs 1 48.959123999999974 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.593 2.778 36 R 0.872 3.616 44 I 0.999** 3.996 46 T 1.000** 3.997 63 Q 0.845 3.533 75 Q 0.566 2.697 78 Y 0.709 3.125 107 E 0.998** 3.991 110 C 0.955* 3.863 126 T 1.000** 3.998 128 E 0.969* 3.905 156 K 0.705 3.114 176 P 0.761 3.283 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: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.513 2.543 +- 1.562 36 R 0.824 3.594 +- 1.331 44 I 0.999** 4.201 +- 0.684 46 T 0.999** 4.203 +- 0.680 63 Q 0.812 3.580 +- 1.377 75 Q 0.505 2.550 +- 1.596 78 Y 0.636 2.955 +- 1.558 107 E 0.997** 4.194 +- 0.699 110 C 0.941 4.004 +- 0.994 126 T 1.000** 4.204 +- 0.677 128 E 0.960* 4.070 +- 0.910 156 K 0.630 2.939 +- 1.563 176 P 0.705 3.207 +- 1.524 Model 8 vs 7 53.93239799999992 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.730 2.730 21 G 0.620 2.447 36 R 0.916 3.192 44 I 0.999** 3.397 46 T 1.000** 3.398 63 Q 0.888 3.119 75 Q 0.685 2.612 78 Y 0.813 2.937 107 E 0.998** 3.394 110 C 0.970* 3.324 126 T 1.000** 3.399 128 E 0.978* 3.345 156 K 0.807 2.918 176 P 0.848 3.020 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: S5_SFBB1) Pr(w>1) post mean +- SE for w 8 L 0.648 2.455 +- 1.250 21 G 0.550 2.190 +- 1.271 36 R 0.878 3.129 +- 1.032 44 I 0.999** 3.484 +- 0.676 46 T 0.999** 3.485 +- 0.674 63 Q 0.858 3.086 +- 1.092 75 Q 0.622 2.402 +- 1.292 78 Y 0.745 2.738 +- 1.204 107 E 0.997** 3.478 +- 0.685 110 C 0.960* 3.373 +- 0.829 126 T 1.000** 3.486 +- 0.673 128 E 0.971* 3.407 +- 0.789 156 K 0.737 2.717 +- 1.218 176 P 0.799 2.906 +- 1.171