--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Mon Dec 11 12:36:20 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/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet/Paxi_S19_20/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/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -14047.73 -14074.62 2 -14047.44 -14069.20 -------------------------------------- TOTAL -14047.58 -14073.94 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet/Paxi_S19_20/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/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.598672 0.012868 3.368540 3.809873 3.596539 1053.88 1106.94 1.000 r(A<->C){all} 0.139015 0.000096 0.119115 0.157120 0.138698 536.25 747.04 1.000 r(A<->G){all} 0.290778 0.000202 0.263196 0.317902 0.290555 618.79 659.38 1.000 r(A<->T){all} 0.096929 0.000042 0.084577 0.109928 0.096644 663.91 841.25 1.000 r(C<->G){all} 0.128216 0.000119 0.106659 0.148599 0.128136 528.78 592.09 1.000 r(C<->T){all} 0.266421 0.000168 0.240283 0.290463 0.265949 649.73 664.99 1.001 r(G<->T){all} 0.078641 0.000045 0.063917 0.090635 0.078496 920.81 936.48 1.000 pi(A){all} 0.307996 0.000087 0.289404 0.325417 0.308023 862.37 865.16 1.000 pi(C){all} 0.170940 0.000053 0.156548 0.185019 0.170769 801.50 850.29 1.000 pi(G){all} 0.190601 0.000061 0.175721 0.206406 0.190478 798.49 810.74 1.001 pi(T){all} 0.330462 0.000095 0.311838 0.349714 0.330531 740.28 804.73 1.000 alpha{1,2} 1.219535 0.021686 0.944315 1.502689 1.201737 1206.88 1222.70 1.000 alpha{3} 4.153370 0.614768 2.807966 5.784710 4.079843 1327.83 1376.67 1.000 pinvar{all} 0.033503 0.000354 0.000498 0.067122 0.031850 1186.02 1234.78 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 -11413.08794 Model 2: PositiveSelection -11410.099548 Model 0: one-ratio -11596.942392 Model 3: discrete -11371.713279 Model 7: beta -11389.075708 Model 8: beta&w>1 -11372.060231 Model 0 vs 1 367.7089040000028 Model 2 vs 1 5.976783999998588 Model 8 vs 7 34.03095400000166 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 1_Paxillaris_S19_FBX1_AB933053) Pr(w>1) post mean +- SE for w 15 A 0.594 1.118 25 T 0.742 1.244 28 F 0.974* 1.428 42 Y 0.966* 1.421 44 F 0.984* 1.435 74 S 0.536 1.081 75 A 0.644 1.169 77 V 0.815 1.305 94 S 0.985* 1.435 95 L 0.982* 1.434 96 T 0.669 1.185 124 S 0.554 1.088 136 A 0.713 1.221 149 K 0.948 1.407 152 D 0.727 1.232 155 M 0.928 1.392 174 F 0.990** 1.440 177 W 0.930 1.393 178 L 0.658 1.176 193 D 0.894 1.365 194 V 0.941 1.402 207 N 0.791 1.283 238 M 0.747 1.250 240 S 0.601 1.129 243 T 0.801 1.293 312 E 0.727 1.235 325 A 0.972* 1.426 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: 1_Paxillaris_S19_FBX1_AB933053) Pr(w>1) post mean +- SE for w 28 F 0.886 1.435 +- 0.247 42 Y 0.868 1.422 +- 0.265 44 F 0.924 1.461 +- 0.215 77 V 0.529 1.167 +- 0.376 94 S 0.922 1.461 +- 0.215 95 L 0.915 1.456 +- 0.222 149 K 0.797 1.369 +- 0.300 155 M 0.756 1.337 +- 0.325 174 F 0.947 1.478 +- 0.189 177 W 0.756 1.338 +- 0.322 193 D 0.688 1.286 +- 0.355 194 V 0.791 1.365 +- 0.310 207 N 0.517 1.147 +- 0.385 243 T 0.511 1.148 +- 0.377 325 A 0.878 1.429 +- 0.253