--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sun Jan 28 05:01:24 WET 2018 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=/usr/bin/ input.sequences= mrbayes.pburnin=2500 mrbayes.bin=mb tcoffee.bin=t_coffee mrbayes.dir=/usr/bin/ tcoffee.dir= tcoffee.minScore=3 input.fasta=/opt/ADOPS/HIV1_N1/GAG_1_3/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_3/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/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -17439.59 -17491.80 2 -17441.55 -17483.87 -------------------------------------- TOTAL -17440.15 -17491.10 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_3/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/ADOPS/HIV1_N1/GAG_1_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.665210 0.017469 3.408917 3.924786 3.663371 1014.55 1113.01 1.000 r(A<->C){all} 0.085257 0.000028 0.074599 0.095353 0.085191 578.37 693.04 1.000 r(A<->G){all} 0.302350 0.000248 0.271668 0.333539 0.302333 174.99 217.26 1.001 r(A<->T){all} 0.043506 0.000016 0.036205 0.051691 0.043459 857.04 872.90 1.002 r(C<->G){all} 0.050841 0.000028 0.041122 0.061631 0.050633 840.14 843.58 1.000 r(C<->T){all} 0.451794 0.000330 0.414924 0.485958 0.451815 183.58 227.23 1.001 r(G<->T){all} 0.066252 0.000041 0.053859 0.078976 0.066211 616.08 649.30 1.005 pi(A){all} 0.413172 0.000089 0.394282 0.431264 0.413102 711.07 730.52 1.000 pi(C){all} 0.200829 0.000057 0.186678 0.216176 0.200821 504.44 578.66 1.000 pi(G){all} 0.208460 0.000063 0.192474 0.223696 0.208426 554.04 623.38 1.000 pi(T){all} 0.177539 0.000058 0.162696 0.192125 0.177546 446.82 521.37 1.000 alpha{1,2} 0.327520 0.000451 0.286598 0.368909 0.326647 1070.34 1132.39 1.000 alpha{3} 2.546008 0.106460 1.945496 3.213376 2.528353 1335.19 1338.71 1.000 pinvar{all} 0.199450 0.000453 0.159863 0.243377 0.199033 1075.99 1136.74 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 -15404.232647 Model 2: PositiveSelection -15340.797519 Model 0: one-ratio -16230.792918 Model 3: discrete -15268.416895 Model 7: beta -15312.704747 Model 8: beta&w>1 -15254.597723 Model 0 vs 1 1653.120541999997 Model 2 vs 1 126.87025600000197 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: B.CY.07.CY201.JF683753_) Pr(w>1) post mean +- SE for w 77 Y 1.000** 3.067 82 V 1.000** 3.067 89 K 1.000** 3.067 91 E 0.972* 3.010 113 A 0.976* 3.017 134 P 1.000** 3.067 203 L 0.966* 2.996 211 I 0.684 2.414 240 N 0.997** 3.062 320 T 0.611 2.264 345 S 0.995** 3.058 360 N 1.000** 3.067 371 Q 0.931 2.924 447 Q 0.594 2.229 452 S 0.945 2.954 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: B.CY.07.CY201.JF683753_) Pr(w>1) post mean +- SE for w 77 Y 1.000** 3.326 +- 0.379 82 V 1.000** 3.326 +- 0.380 89 K 1.000** 3.326 +- 0.379 91 E 0.957* 3.221 +- 0.602 113 A 0.968* 3.248 +- 0.556 134 P 1.000** 3.326 +- 0.379 203 L 0.959* 3.228 +- 0.593 211 I 0.588 2.329 +- 1.159 240 N 0.997** 3.319 +- 0.400 320 T 0.549 2.248 +- 1.172 345 S 0.995** 3.315 +- 0.411 360 N 1.000** 3.326 +- 0.380 371 Q 0.923 3.143 +- 0.721 447 Q 0.546 2.244 +- 1.176 452 S 0.934 3.168 +- 0.686 Model 8 vs 7 116.214047999998 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: B.CY.07.CY201.JF683753_) Pr(w>1) post mean +- SE for w 77 Y 1.000** 2.453 82 V 1.000** 2.453 88 Q 0.515 1.695 89 K 1.000** 2.453 91 E 0.981* 2.423 113 A 0.983* 2.427 134 P 1.000** 2.453 203 L 0.976* 2.415 211 I 0.813 2.161 240 N 0.998** 2.449 320 T 0.767 2.087 345 S 0.997** 2.447 360 N 1.000** 2.452 371 Q 0.942 2.363 447 Q 0.720 2.011 452 S 0.968* 2.402 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: B.CY.07.CY201.JF683753_) Pr(w>1) post mean +- SE for w 77 Y 1.000** 2.500 +- 0.005 82 V 1.000** 2.500 +- 0.013 88 Q 0.551 1.791 +- 0.787 89 K 1.000** 2.500 +- 0.006 91 E 0.982* 2.472 +- 0.208 113 A 0.985* 2.477 +- 0.188 134 P 1.000** 2.500 +- 0.006 203 L 0.979* 2.468 +- 0.223 211 I 0.842 2.251 +- 0.577 240 N 0.998** 2.496 +- 0.074 320 T 0.811 2.200 +- 0.624 345 S 0.997** 2.495 +- 0.086 360 N 1.000** 2.500 +- 0.023 371 Q 0.954* 2.427 +- 0.331 447 Q 0.775 2.140 +- 0.669 452 S 0.973* 2.458 +- 0.254