--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Nov 08 17:59:26 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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazermus/S24_16SFBBs/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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -7156.56 -7175.36 2 -7156.20 -7173.61 -------------------------------------- TOTAL -7156.36 -7174.83 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/afazermus/S24_16SFBBs/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/afazermus/S24_16SFBBs/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 1.447229 0.003634 1.335770 1.566210 1.445050 1351.76 1414.83 1.001 r(A<->C){all} 0.120002 0.000147 0.097347 0.144671 0.119452 958.31 1019.37 1.000 r(A<->G){all} 0.301393 0.000377 0.262879 0.338095 0.301383 833.96 869.29 1.000 r(A<->T){all} 0.073112 0.000057 0.058621 0.088271 0.072840 1020.27 1176.74 1.000 r(C<->G){all} 0.155235 0.000242 0.126814 0.187189 0.154745 798.29 911.43 1.000 r(C<->T){all} 0.266778 0.000335 0.231695 0.302710 0.266908 599.68 802.36 1.000 r(G<->T){all} 0.083479 0.000081 0.067219 0.102213 0.083106 1111.91 1177.96 1.001 pi(A){all} 0.294061 0.000116 0.272596 0.315150 0.293560 958.74 1012.23 1.001 pi(C){all} 0.174792 0.000078 0.158384 0.193011 0.174467 984.84 1128.72 1.000 pi(G){all} 0.196583 0.000087 0.178343 0.214911 0.196544 944.00 1109.73 1.003 pi(T){all} 0.334565 0.000127 0.312746 0.356465 0.334628 1035.74 1084.72 1.000 alpha{1,2} 0.789860 0.014972 0.581482 1.035847 0.771309 1223.48 1362.24 1.000 alpha{3} 2.500810 0.495852 1.361102 3.924254 2.362617 1300.59 1331.61 1.000 pinvar{all} 0.050565 0.001313 0.000006 0.119193 0.043952 964.62 1226.54 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 -5182.219563 Model 2: PositiveSelection -5153.400929 Model 0: one-ratio -5293.71354 Model 3: discrete -5153.186482 Model 7: beta -5190.523449 Model 8: beta&w>1 -5153.987351 Model 0 vs 1 222.98795400000017 Model 2 vs 1 57.637267999998585 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S24_SFBB1) Pr(w>1) post mean +- SE for w 14 N 0.993** 3.468 20 R 0.999** 3.483 24 P 0.973* 3.419 53 L 0.956* 3.375 60 E 0.918 3.281 72 L 0.635 2.578 101 R 0.829 3.059 109 I 0.999** 3.482 111 T 0.999** 3.483 128 Q 0.882 3.191 172 E 0.966* 3.401 174 C 0.853 3.119 190 T 0.998** 3.481 192 E 0.809 3.010 220 K 0.528 2.312 243 T 0.745 2.851 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: S24_SFBB1) Pr(w>1) post mean +- SE for w 14 N 0.992** 3.589 +- 0.472 20 R 0.999** 3.609 +- 0.416 24 P 0.967* 3.522 +- 0.615 53 L 0.947 3.469 +- 0.708 60 E 0.905 3.362 +- 0.857 72 L 0.577 2.467 +- 1.288 101 R 0.790 3.041 +- 1.108 109 I 0.998** 3.607 +- 0.423 111 T 0.999** 3.609 +- 0.417 128 Q 0.864 3.253 +- 0.970 172 E 0.957* 3.493 +- 0.663 174 C 0.825 3.143 +- 1.051 190 T 0.998** 3.606 +- 0.426 192 E 0.771 2.994 +- 1.140 243 T 0.686 2.752 +- 1.224 Model 8 vs 7 73.07219600000099 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: S24_SFBB1) Pr(w>1) post mean +- SE for w 14 N 0.997** 3.021 20 R 1.000** 3.025 24 P 0.990* 3.005 53 L 0.981* 2.986 58 F 0.667 2.313 60 E 0.959* 2.939 72 L 0.833 2.668 101 R 0.927 2.870 109 I 0.999** 3.025 111 T 1.000** 3.025 128 Q 0.937 2.891 140 Q 0.614 2.183 143 Y 0.596 2.159 157 T 0.690 2.353 172 E 0.988* 3.000 174 C 0.934 2.884 190 T 0.999** 3.024 192 E 0.912 2.836 220 K 0.754 2.496 237 C 0.620 2.214 243 T 0.901 2.815 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: S24_SFBB1) Pr(w>1) post mean +- SE for w 14 N 0.998** 2.826 +- 0.509 20 R 1.000** 2.831 +- 0.502 24 P 0.990* 2.809 +- 0.533 53 L 0.981* 2.790 +- 0.559 58 F 0.718 2.163 +- 0.870 60 E 0.961* 2.746 +- 0.615 72 L 0.840 2.449 +- 0.801 73 A 0.583 1.883 +- 0.922 85 G 0.505 1.727 +- 0.957 101 R 0.926 2.657 +- 0.684 109 I 0.999** 2.830 +- 0.503 111 T 1.000** 2.831 +- 0.503 128 Q 0.940 2.698 +- 0.667 140 Q 0.669 2.079 +- 0.943 143 Y 0.674 2.073 +- 0.889 157 T 0.727 2.202 +- 0.911 172 E 0.987* 2.802 +- 0.540 174 C 0.936 2.683 +- 0.669 190 T 0.999** 2.830 +- 0.505 192 E 0.913 2.628 +- 0.712 220 K 0.776 2.303 +- 0.859 237 C 0.688 2.091 +- 0.867 243 T 0.896 2.580 +- 0.725