--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Tue Mar 20 06:56:20 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_A1/GAG_1_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_5/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_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -18327.21 -18371.35 2 -18328.67 -18370.91 -------------------------------------- TOTAL -18327.69 -18371.15 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_A1/GAG_1_5/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_A1/GAG_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.935858 0.019342 3.659284 4.208033 3.934342 802.94 953.12 1.001 r(A<->C){all} 0.091202 0.000032 0.080702 0.102607 0.091094 625.31 741.28 1.000 r(A<->G){all} 0.312617 0.000242 0.282560 0.341310 0.312783 425.33 432.79 1.000 r(A<->T){all} 0.045048 0.000017 0.036403 0.052688 0.044911 833.07 840.70 1.001 r(C<->G){all} 0.048697 0.000026 0.038817 0.057999 0.048721 599.23 717.89 1.000 r(C<->T){all} 0.428210 0.000306 0.395412 0.463020 0.428166 402.35 415.21 1.000 r(G<->T){all} 0.074225 0.000043 0.061397 0.086894 0.073858 635.35 738.43 1.000 pi(A){all} 0.398270 0.000084 0.380658 0.416867 0.398367 611.99 737.75 1.000 pi(C){all} 0.206623 0.000065 0.191095 0.222220 0.206496 477.62 519.09 1.000 pi(G){all} 0.214060 0.000060 0.199768 0.229666 0.214065 562.29 621.94 1.000 pi(T){all} 0.181047 0.000057 0.166452 0.195647 0.180959 693.59 749.56 1.000 alpha{1,2} 0.300114 0.000378 0.263201 0.337521 0.299038 1048.79 1189.67 1.000 alpha{3} 1.736297 0.040599 1.361735 2.131270 1.724120 1168.17 1203.51 1.001 pinvar{all} 0.149418 0.000584 0.101102 0.195927 0.149388 1075.33 1103.82 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 -15275.88814 Model 2: PositiveSelection -15214.968097 Model 0: one-ratio -16149.492641 Model 3: discrete -15140.327268 Model 7: beta -15179.162644 Model 8: beta&w>1 -15120.366518 Model 0 vs 1 1747.2090020000032 Model 2 vs 1 121.84008599999652 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.TH.00.C015F1P190.GU458453_) Pr(w>1) post mean +- SE for w 28 Q 0.774 2.461 59 I 0.984* 2.858 65 T 0.982* 2.854 77 Y 0.985* 2.860 82 T 1.000** 2.888 89 R 1.000** 2.888 91 D 0.608 2.148 129 S 0.999** 2.887 198 V 0.999** 2.887 206 I 0.976* 2.842 235 S 1.000** 2.888 354 A 0.949 2.792 355 N 1.000** 2.887 441 V 0.758 2.431 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: 01_AE.TH.00.C015F1P190.GU458453_) Pr(w>1) post mean +- SE for w 28 Q 0.753 2.218 +- 0.750 59 I 0.979* 2.707 +- 0.491 65 T 0.978* 2.711 +- 0.498 77 Y 0.982* 2.718 +- 0.487 82 T 1.000** 2.749 +- 0.433 89 R 1.000** 2.749 +- 0.433 91 D 0.630 2.000 +- 0.798 129 S 0.999** 2.748 +- 0.436 198 V 0.999** 2.748 +- 0.435 206 I 0.971* 2.696 +- 0.514 235 S 1.000** 2.749 +- 0.433 354 A 0.937 2.617 +- 0.584 355 N 0.999** 2.748 +- 0.435 441 V 0.746 2.253 +- 0.803 Model 8 vs 7 117.59225199999855 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: 01_AE.TH.00.C015F1P190.GU458453_) Pr(w>1) post mean +- SE for w 28 Q 0.923 2.200 59 I 0.993** 2.303 65 T 0.992** 2.301 77 Y 0.993** 2.302 82 T 1.000** 2.312 89 R 1.000** 2.312 91 D 0.842 2.082 129 S 1.000** 2.312 198 V 1.000** 2.312 206 I 0.990* 2.298 235 S 1.000** 2.312 354 A 0.983* 2.287 355 N 1.000** 2.312 441 V 0.903 2.171 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: 01_AE.TH.00.C015F1P190.GU458453_) Pr(w>1) post mean +- SE for w 28 Q 0.833 2.238 +- 0.585 59 I 0.988* 2.481 +- 0.173 65 T 0.991** 2.486 +- 0.150 77 Y 0.992** 2.487 +- 0.143 82 T 1.000** 2.500 +- 0.006 89 R 1.000** 2.500 +- 0.015 91 D 0.734 2.081 +- 0.697 129 S 1.000** 2.499 +- 0.030 198 V 1.000** 2.499 +- 0.032 206 I 0.986* 2.477 +- 0.187 235 S 1.000** 2.500 +- 0.003 354 A 0.967* 2.448 +- 0.280 355 N 1.000** 2.499 +- 0.030 441 V 0.872 2.297 +- 0.530