--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Wed Apr 11 16:20:23 WEST 2018 codeml.models=1 2 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 tcoffee.bin=t_coffee mrbayes.dir= tcoffee.dir= tcoffee.minScore=3 input.fasta= input.names= mrbayes.params= codeml.params= --- PSRF SUMMARY Estimated marginal likelihoods for runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Use the harmonic mean for Bayes factor comparisons of models) Run Arithmetic mean Harmonic mean -------------------------------------- 1 -5909.40 -5935.27 2 -5909.37 -5931.65 -------------------------------------- TOTAL -5909.38 -5934.61 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-A/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p": (Summaries are based on a total of 15002 samples from 2 runs) (Each run produced 10001 samples of which 7501 samples were included) 95% Cred. Interval ---------------------- Parameter Mean Variance Lower Upper Median PSRF * --------------------------------------------------------------------------------------------- TL{all} 1.109961 0.003825 0.994000 1.239000 1.108000 1.000 r(A<->C){all} 0.095601 0.000166 0.072136 0.122642 0.095061 1.000 r(A<->G){all} 0.279253 0.000490 0.238371 0.324604 0.278602 1.001 r(A<->T){all} 0.193750 0.000547 0.150107 0.240722 0.192812 1.000 r(C<->G){all} 0.091954 0.000101 0.073221 0.112563 0.091674 1.000 r(C<->T){all} 0.257683 0.000498 0.216122 0.302160 0.257316 1.000 r(G<->T){all} 0.081758 0.000149 0.059002 0.107330 0.081475 1.000 pi(A){all} 0.202443 0.000118 0.181573 0.224377 0.202373 1.002 pi(C){all} 0.298799 0.000149 0.274967 0.323140 0.298940 1.001 pi(G){all} 0.329078 0.000162 0.304693 0.354435 0.329070 1.000 pi(T){all} 0.169681 0.000106 0.149769 0.190551 0.169556 1.000 alpha{1,2} 0.472662 0.008433 0.318552 0.679073 0.463913 1.001 alpha{3} 29.894653 2476.758009 1.391730 178.022267 4.640338 1.005 pinvar{all} 0.312287 0.003464 0.183530 0.408660 0.318791 1.001 --------------------------------------------------------------------------------------------- * Convergence diagnostic (PSRF = Potential scale reduction factor [Gelman and Rubin, 1992], uncorrected) should approach 1 as runs converge. The values may be unreliable if you have a small number of samples. PSRF should only be used as a rough guide to convergence since all the assumptions that allow one to interpret it as a scale reduction factor are not met in the phylogenetic context. --- CODEML SUMMARY Model 8: beta&w>1 -5759.42454 Model 7: beta -5841.633019 Model 1: NearlyNeutral -5834.894205 Model 2: PositiveSelection -5761.132259 Model 2 vs 1 147.52389199999925 Additional information for M1 vs M2: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_002107.3_HLA-A) Pr(w>1) post mean +- SE for w 30 F 0.986* 5.076 45 A 0.999** 5.131 83 Q 0.780 4.225 84 E 0.988* 5.086 87 N 1.000** 5.134 88 V 0.934 4.861 94 T 0.970* 5.012 98 D 0.999** 5.132 118 I 1.000** 5.134 135 R 1.000** 5.134 137 D 0.999** 5.130 172 H 0.998** 5.128 173 E 0.997** 5.120 177 L 1.000** 5.134 184 T 1.000** 5.134 318 T 0.833 4.443 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: Homo_sapiens_Hominidae_Haplorrhini_NP_002107.3_HLA-A) Pr(w>1) post mean +- SE for w 30 F 0.987* 5.061 +- 0.722 45 A 0.999** 5.113 +- 0.569 83 Q 0.798 4.241 +- 1.699 84 E 0.990* 5.073 +- 0.691 87 N 1.000** 5.116 +- 0.559 88 V 0.942 4.868 +- 1.102 94 T 0.974* 5.008 +- 0.853 98 D 0.999** 5.113 +- 0.567 118 I 1.000** 5.116 +- 0.558 135 R 1.000** 5.116 +- 0.558 137 D 0.999** 5.112 +- 0.572 172 H 0.999** 5.110 +- 0.579 173 E 0.997** 5.104 +- 0.600 177 L 1.000** 5.116 +- 0.558 184 T 1.000** 5.115 +- 0.560 316 A 0.548 3.221 +- 2.060 318 T 0.854 4.505 +- 1.536 Model 8 vs 7 164.4169579999998 Additional information for M7 vs M8: Naive Empirical Bayes (NEB) analysis Positively selected sites (*: P>95%; **: P>99%) (amino acids refer to 1st sequence: Homo_sapiens_Hominidae_Haplorrhini_NP_002107.3_HLA-A) Pr(w>1) post mean +- SE for w 30 F 0.994** 4.532 45 A 1.000** 4.552 83 Q 0.901 4.192 84 E 0.995** 4.535 87 N 1.000** 4.554 88 V 0.970* 4.444 91 Q 0.548 2.898 94 T 0.986* 4.501 98 D 1.000** 4.553 118 I 1.000** 4.554 135 R 1.000** 4.554 137 D 1.000** 4.552 172 H 0.999** 4.551 173 E 0.998** 4.548 177 L 1.000** 4.554 184 T 1.000** 4.554 316 A 0.639 3.209 318 T 0.906 4.205 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: Homo_sapiens_Hominidae_Haplorrhini_NP_002107.3_HLA-A) Pr(w>1) post mean +- SE for w 30 F 0.993** 4.606 +- 0.500 45 A 1.000** 4.631 +- 0.406 83 Q 0.883 4.176 +- 1.247 84 E 0.994** 4.611 +- 0.484 87 N 1.000** 4.632 +- 0.399 88 V 0.967* 4.505 +- 0.775 91 Q 0.518 2.781 +- 1.846 94 T 0.984* 4.573 +- 0.610 98 D 1.000** 4.631 +- 0.404 118 I 1.000** 4.632 +- 0.398 135 R 1.000** 4.632 +- 0.399 137 D 0.999** 4.630 +- 0.407 172 H 0.999** 4.629 +- 0.413 173 E 0.998** 4.626 +- 0.426 177 L 1.000** 4.632 +- 0.398 184 T 1.000** 4.632 +- 0.400 316 A 0.617 3.159 +- 1.865 318 T 0.898 4.243 +- 1.203