--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Jan 27 09:17:35 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_1/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS/HIV1_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -18272.33 -18319.14 2 -18273.56 -18313.19 -------------------------------------- TOTAL -18272.77 -18318.45 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS/HIV1_N1/GAG_1_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/HIV1_N1/GAG_1_1/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_1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat". 95% HPD Interval -------------------- Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+ ------------------------------------------------------------------------------------------------------ TL{all} 3.935340 0.019459 3.659520 4.203024 3.935345 1223.88 1300.51 1.000 r(A<->C){all} 0.087036 0.000029 0.077142 0.098518 0.086923 708.97 716.90 1.000 r(A<->G){all} 0.309475 0.000224 0.279997 0.337671 0.309110 296.43 386.32 1.000 r(A<->T){all} 0.045167 0.000017 0.037245 0.053086 0.045104 667.74 836.36 1.000 r(C<->G){all} 0.043314 0.000025 0.033523 0.052731 0.043060 565.03 718.61 1.000 r(C<->T){all} 0.435891 0.000308 0.400834 0.467960 0.436154 307.19 373.02 1.000 r(G<->T){all} 0.079117 0.000048 0.065913 0.092391 0.079029 614.51 669.83 1.000 pi(A){all} 0.398392 0.000080 0.381733 0.416692 0.398541 763.25 774.72 1.000 pi(C){all} 0.205047 0.000057 0.190982 0.220586 0.204874 534.57 687.05 1.000 pi(G){all} 0.218028 0.000061 0.203262 0.233594 0.217976 532.13 591.87 1.000 pi(T){all} 0.178532 0.000051 0.163902 0.191875 0.178439 476.21 599.20 1.000 alpha{1,2} 0.342905 0.000510 0.297558 0.384129 0.341400 1003.47 1088.03 1.000 alpha{3} 1.906849 0.051151 1.461061 2.325904 1.897151 1414.61 1433.47 1.000 pinvar{all} 0.162694 0.000527 0.117398 0.206237 0.163032 958.43 1067.22 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 -16324.941755 Model 2: PositiveSelection -16268.105319 Model 0: one-ratio -17178.663071 Model 3: discrete -16203.783623 Model 7: beta -16231.126789 Model 8: beta&w>1 -16173.827495 Model 0 vs 1 1707.4426319999984 Model 2 vs 1 113.67287199999919 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: BC.CN.07.07CNYN367.KF835544_) Pr(w>1) post mean +- SE for w 77 Y 0.973* 2.688 82 T 1.000** 2.734 89 G 0.999** 2.733 91 E 0.854 2.481 115 T 1.000** 2.735 134 P 0.993** 2.723 201 T 0.987* 2.712 209 V 0.920 2.595 238 S 1.000** 2.734 358 S 1.000** 2.734 359 A 0.987* 2.713 370 P 0.530 1.919 424 H 0.778 2.350 445 S 0.725 2.258 451 P 0.998** 2.731 455 P 0.986* 2.711 457 L 0.572 1.993 458 T 0.580 2.006 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: BC.CN.07.07CNYN367.KF835544_) Pr(w>1) post mean +- SE for w 77 Y 0.968* 2.469 +- 0.299 82 T 1.000** 2.518 +- 0.134 89 G 0.999** 2.517 +- 0.143 91 E 0.874 2.320 +- 0.510 115 T 1.000** 2.518 +- 0.134 116 I 0.529 1.797 +- 0.755 134 P 0.991** 2.504 +- 0.196 201 T 0.983* 2.493 +- 0.235 209 V 0.919 2.393 +- 0.430 238 S 0.999** 2.517 +- 0.139 358 S 1.000** 2.518 +- 0.137 359 A 0.985* 2.496 +- 0.225 370 P 0.561 1.846 +- 0.751 424 H 0.797 2.203 +- 0.615 445 S 0.754 2.138 +- 0.654 451 P 0.997** 2.514 +- 0.156 455 P 0.982* 2.491 +- 0.242 457 L 0.606 1.913 +- 0.740 458 T 0.613 1.925 +- 0.737 Model 8 vs 7 114.59858800000075 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: BC.CN.07.07CNYN367.KF835544_) Pr(w>1) post mean +- SE for w 13 K 0.692 1.767 65 A 0.517 1.527 77 Y 0.988* 2.148 82 T 1.000** 2.163 89 G 1.000** 2.162 91 E 0.954* 2.104 115 T 1.000** 2.163 116 I 0.771 1.864 126 L 0.685 1.754 134 P 0.997** 2.159 201 T 0.993** 2.154 209 V 0.971* 2.125 238 S 1.000** 2.163 266 T 0.547 1.567 358 S 1.000** 2.163 359 A 0.994** 2.156 370 P 0.746 1.831 424 H 0.914 2.051 445 S 0.900 2.033 451 P 0.999** 2.161 455 P 0.993** 2.153 457 L 0.812 1.919 458 T 0.832 1.944 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: BC.CN.07.07CNYN367.KF835544_) Pr(w>1) post mean +- SE for w 77 Y 0.982* 2.471 +- 0.212 82 T 1.000** 2.500 +- 0.007 89 G 0.999** 2.499 +- 0.042 91 E 0.865 2.288 +- 0.536 115 T 1.000** 2.500 +- 0.005 116 I 0.618 1.892 +- 0.774 134 P 0.996** 2.494 +- 0.099 201 T 0.990* 2.484 +- 0.158 209 V 0.938 2.403 +- 0.378 238 S 1.000** 2.499 +- 0.031 358 S 1.000** 2.500 +- 0.025 359 A 0.989* 2.483 +- 0.163 370 P 0.576 1.826 +- 0.788 424 H 0.809 2.199 +- 0.620 445 S 0.775 2.145 +- 0.659 451 P 0.999** 2.498 +- 0.058 455 P 0.990* 2.484 +- 0.157 457 L 0.658 1.958 +- 0.753 458 T 0.692 2.011 +- 0.733