--- EXPERIMENT NOTES --- EXPERIMENT PROPERTIES #Thu Apr 12 00:52:40 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-DRB5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB5/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 -2070.09 -2086.67 2 -2070.24 -2083.84 -------------------------------------- TOTAL -2070.16 -2086.03 -------------------------------------- Model parameter summaries over the runs sampled in files "/home/jorge/Data/ADOPS/HLA/HLA-DRB5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/home/jorge/Data/ADOPS/HLA/HLA-DRB5/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} 0.387002 0.002772 0.302000 0.506000 0.381000 1.002 r(A<->C){all} 0.063303 0.000621 0.021490 0.117950 0.060938 1.000 r(A<->G){all} 0.298973 0.001963 0.216633 0.390808 0.297989 1.000 r(A<->T){all} 0.103916 0.001019 0.049369 0.171716 0.101087 1.001 r(C<->G){all} 0.097919 0.000523 0.057623 0.147252 0.096397 1.000 r(C<->T){all} 0.366160 0.002758 0.268401 0.474117 0.364419 1.000 r(G<->T){all} 0.069729 0.000452 0.033963 0.117084 0.067622 1.000 pi(A){all} 0.223771 0.000189 0.197390 0.251420 0.223506 1.000 pi(C){all} 0.252485 0.000208 0.224846 0.281379 0.252357 1.000 pi(G){all} 0.319789 0.000228 0.290485 0.349826 0.319538 1.000 pi(T){all} 0.203956 0.000181 0.178250 0.231141 0.203611 1.000 alpha{1,2} 28.031627 2721.559097 0.308864 180.764229 1.105597 1.012 alpha{3} 101.990667 3266.394053 6.809541 195.003643 100.976671 1.000 pinvar{all} 0.607037 0.006145 0.427042 0.720997 0.620129 1.007 --------------------------------------------------------------------------------------------- * 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 -2002.415363 Model 7: beta -2013.086717 Model 1: NearlyNeutral -2012.263927 Model 2: PositiveSelection -2002.425163 Model 2 vs 1 19.67752799999971 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_002116.2_HLA-DRB5) Pr(w>1) post mean +- SE for w 3 C 0.593 3.085 14 K 0.962* 4.446 38 Q 0.647 3.312 42 Y 0.929 4.329 55 F 0.963* 4.451 59 D 0.885 4.171 66 D 0.730 3.610 67 L 0.847 4.030 95 F 0.961* 4.442 98 D 0.992** 4.554 99 R 0.641 3.255 102 A 0.727 3.599 106 Y 0.939 4.363 114 G 0.961* 4.442 118 T 0.733 3.607 124 E 0.906 4.248 185 T 0.580 3.035 243 A 0.786 3.812 259 H 0.536 2.870 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_002116.2_HLA-DRB5) Pr(w>1) post mean +- SE for w 14 K 0.939 5.211 +- 2.037 38 Q 0.517 2.982 +- 2.230 42 Y 0.897 5.014 +- 2.172 55 F 0.949 5.278 +- 2.013 59 D 0.787 4.346 +- 2.291 66 D 0.595 3.358 +- 2.306 67 L 0.798 4.527 +- 2.395 95 F 0.943 5.246 +- 2.030 98 D 0.989* 5.475 +- 1.846 99 R 0.530 3.083 +- 2.368 102 A 0.595 3.367 +- 2.316 106 Y 0.897 4.986 +- 2.148 114 G 0.941 5.235 +- 2.035 118 T 0.629 3.585 +- 2.429 124 E 0.821 4.530 +- 2.253 243 A 0.662 3.705 +- 2.351 Model 8 vs 7 21.342707999999675 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_002116.2_HLA-DRB5) Pr(w>1) post mean +- SE for w 3 C 0.661 3.108 14 K 0.985* 4.340 38 Q 0.757 3.486 40 D 0.534 2.622 42 Y 0.963* 4.256 55 F 0.985* 4.339 59 D 0.951* 4.212 66 D 0.828 3.750 67 L 0.901 4.022 95 F 0.984* 4.336 98 D 0.997** 4.384 99 R 0.692 3.221 102 A 0.825 3.740 106 Y 0.971* 4.287 114 G 0.985* 4.337 118 T 0.797 3.625 124 E 0.962* 4.252 185 T 0.644 3.043 243 A 0.871 3.914 259 H 0.603 2.885 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_002116.2_HLA-DRB5) Pr(w>1) post mean +- SE for w 3 C 0.571 2.856 +- 2.258 14 K 0.975* 4.930 +- 1.855 38 Q 0.640 3.168 +- 2.234 42 Y 0.946 4.797 +- 1.964 55 F 0.978* 4.949 +- 1.848 59 D 0.898 4.509 +- 2.057 66 D 0.719 3.569 +- 2.253 67 L 0.870 4.438 +- 2.183 95 F 0.976* 4.937 +- 1.855 98 D 0.996** 5.032 +- 1.772 99 R 0.608 3.059 +- 2.323 102 A 0.719 3.575 +- 2.260 106 Y 0.952* 4.813 +- 1.935 114 G 0.975* 4.934 +- 1.856 118 T 0.720 3.625 +- 2.337 124 E 0.919 4.623 +- 2.009 185 T 0.563 2.833 +- 2.273 243 A 0.782 3.905 +- 2.236 259 H 0.517 2.586 +- 2.178