--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Sat Mar 24 14:59:40 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= 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=/opt/ADOPS1/HIV1_AMINO/POL_1_5/input.fasta input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -31867.45 -31913.67 2 -31866.78 -31913.73 -------------------------------------- TOTAL -31867.06 -31913.70 -------------------------------------- Model parameter summaries over the runs sampled in files "/opt/ADOPS1/HIV1_AMINO/POL_1_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AMINO/POL_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/ADOPS1/HIV1_AMINO/POL_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} 3.418357 0.009402 3.230166 3.617533 3.418511 1310.89 1353.43 1.000 r(A<->C){all} 0.079808 0.000017 0.072261 0.088290 0.079717 534.29 599.90 1.000 r(A<->G){all} 0.363347 0.000167 0.338050 0.387642 0.362953 209.67 283.79 1.000 r(A<->T){all} 0.035486 0.000006 0.030684 0.040567 0.035441 908.84 942.87 1.000 r(C<->G){all} 0.036263 0.000017 0.027865 0.043847 0.036092 569.57 616.00 1.000 r(C<->T){all} 0.448445 0.000186 0.421849 0.474013 0.448931 198.90 291.07 1.001 r(G<->T){all} 0.036651 0.000012 0.030062 0.043475 0.036508 666.35 727.15 1.003 pi(A){all} 0.411384 0.000051 0.397827 0.425843 0.411284 530.99 734.49 1.000 pi(C){all} 0.178748 0.000031 0.168612 0.189812 0.178765 505.31 549.76 1.001 pi(G){all} 0.208938 0.000036 0.197626 0.221079 0.208697 591.99 595.90 1.000 pi(T){all} 0.200930 0.000035 0.189085 0.212477 0.200756 688.03 689.13 1.000 alpha{1,2} 0.283481 0.000253 0.252200 0.313110 0.282770 1024.07 1093.12 1.000 alpha{3} 2.212637 0.050530 1.830136 2.690248 2.189349 1202.43 1237.25 1.001 pinvar{all} 0.265349 0.000354 0.231083 0.305367 0.265586 1084.49 1108.16 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 -31214.748226 Model 2: PositiveSelection -31088.616652 Model 0: one-ratio -32862.797222 Model 3: discrete -30879.558554 Model 7: beta -30961.122093 Model 8: beta&w>1 -30816.421152 Model 0 vs 1 3296.0979920000027 Model 2 vs 1 252.26314799999818 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_) Pr(w>1) post mean +- SE for w 17 P 0.997** 3.112 21 T 0.608 2.290 32 Q 0.939 2.990 34 R 0.960* 3.034 36 L 1.000** 3.120 39 Q 0.781 2.656 41 L 0.789 2.671 42 N 1.000** 3.120 43 F 0.578 2.225 62 I 0.935 2.981 106 P 1.000** 3.120 265 S 1.000** 3.120 304 S 1.000** 3.119 349 E 0.925 2.960 353 K 0.803 2.703 357 T 0.976* 3.070 387 Q 0.989* 3.096 428 T 0.982* 3.080 476 Q 1.000** 3.120 499 M 0.843 2.788 518 A 0.967* 3.049 519 L 1.000** 3.119 610 S 0.999** 3.118 625 Q 1.000** 3.119 633 S 0.999** 3.118 696 K 1.000** 3.120 821 S 0.995** 3.108 826 N 0.994** 3.107 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: C.BR.10.10BR_SP033.KT427810_) Pr(w>1) post mean +- SE for w 17 P 0.998** 3.488 +- 0.145 21 T 0.559 2.393 +- 1.239 32 Q 0.951* 3.371 +- 0.544 34 R 0.964* 3.403 +- 0.472 36 L 1.000** 3.494 +- 0.080 39 Q 0.723 2.802 +- 1.118 41 L 0.756 2.883 +- 1.074 42 N 1.000** 3.494 +- 0.080 43 F 0.557 2.387 +- 1.240 62 I 0.912 3.275 +- 0.709 106 P 1.000** 3.494 +- 0.080 265 S 1.000** 3.494 +- 0.080 304 S 1.000** 3.493 +- 0.091 349 E 0.909 3.268 +- 0.720 353 K 0.798 2.989 +- 1.004 357 T 0.979* 3.441 +- 0.368 387 Q 0.990** 3.469 +- 0.260 428 T 0.984* 3.454 +- 0.321 476 Q 1.000** 3.494 +- 0.080 499 M 0.683 2.701 +- 1.162 518 A 0.969* 3.416 +- 0.440 519 L 1.000** 3.493 +- 0.085 610 S 1.000** 3.493 +- 0.091 625 Q 1.000** 3.493 +- 0.085 633 S 0.999** 3.492 +- 0.102 696 K 1.000** 3.494 +- 0.080 821 S 0.994** 3.480 +- 0.201 826 N 0.994** 3.477 +- 0.215 Model 8 vs 7 289.40188200000557 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: C.BR.10.10BR_SP033.KT427810_) Pr(w>1) post mean +- SE for w 17 P 1.000** 2.587 21 T 0.900 2.403 32 Q 0.984* 2.559 34 R 0.994** 2.577 36 L 1.000** 2.588 39 Q 0.950 2.495 41 L 0.956* 2.507 42 N 1.000** 2.588 43 F 0.846 2.304 62 I 0.992** 2.573 106 P 1.000** 2.588 265 S 1.000** 2.588 304 S 1.000** 2.588 349 E 0.991** 2.571 353 K 0.975* 2.543 357 T 0.997** 2.582 387 Q 0.999** 2.586 428 T 0.998** 2.584 476 Q 1.000** 2.588 499 M 0.990** 2.570 518 A 0.996** 2.580 519 L 1.000** 2.588 610 S 1.000** 2.588 625 Q 1.000** 2.588 633 S 1.000** 2.588 696 K 1.000** 2.588 776 L 0.635 1.906 821 S 1.000** 2.587 826 N 1.000** 2.587 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: C.BR.10.10BR_SP033.KT427810_) Pr(w>1) post mean +- SE for w 17 P 0.999** 2.498 +- 0.054 21 T 0.896 2.332 +- 0.493 32 Q 0.980* 2.467 +- 0.227 34 R 0.989* 2.483 +- 0.163 36 L 1.000** 2.500 +- 0.001 39 Q 0.928 2.385 +- 0.412 41 L 0.944 2.410 +- 0.369 42 N 1.000** 2.500 +- 0.006 43 F 0.860 2.273 +- 0.564 62 I 0.981* 2.470 +- 0.214 106 P 1.000** 2.500 +- 0.001 265 S 1.000** 2.500 +- 0.007 304 S 1.000** 2.500 +- 0.020 349 E 0.976* 2.463 +- 0.240 353 K 0.953* 2.426 +- 0.334 357 T 0.994** 2.490 +- 0.124 387 Q 0.997** 2.495 +- 0.093 428 T 0.995** 2.492 +- 0.110 476 Q 1.000** 2.500 +- 0.003 499 M 0.971* 2.454 +- 0.266 518 A 0.992** 2.487 +- 0.142 519 L 1.000** 2.500 +- 0.012 610 S 1.000** 2.500 +- 0.026 625 Q 1.000** 2.500 +- 0.016 633 S 1.000** 2.499 +- 0.028 696 K 1.000** 2.500 +- 0.001 776 L 0.717 2.029 +- 0.753 821 S 0.998** 2.498 +- 0.063 826 N 0.998** 2.497 +- 0.064