--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 04 21:14:25 WET 2017
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/Ebolaaminoresults/NP/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/NP/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/Ebolaaminoresults/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13482.43 -13527.89
2 -13478.54 -13529.66
--------------------------------------
TOTAL -13479.21 -13529.12
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/NP/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/Ebolaaminoresults/NP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.782656 0.071600 4.263236 5.295523 4.776529 335.61 341.12 1.000
r(A<->C){all} 0.113521 0.000109 0.092684 0.133409 0.113391 606.72 631.09 1.000
r(A<->G){all} 0.327860 0.000313 0.297043 0.365615 0.327233 573.42 594.83 1.000
r(A<->T){all} 0.039268 0.000056 0.024326 0.053888 0.039052 806.01 807.15 1.000
r(C<->G){all} 0.032905 0.000055 0.018677 0.047354 0.032651 832.58 840.53 1.000
r(C<->T){all} 0.439966 0.000367 0.403327 0.477295 0.440132 547.92 699.09 1.000
r(G<->T){all} 0.046480 0.000071 0.029309 0.062410 0.046023 745.42 759.48 1.000
pi(A){all} 0.318097 0.000049 0.303853 0.330969 0.318107 866.01 880.76 1.000
pi(C){all} 0.236239 0.000039 0.224779 0.249001 0.236301 761.38 798.37 1.000
pi(G){all} 0.218912 0.000039 0.207147 0.231711 0.218847 808.25 834.20 1.002
pi(T){all} 0.226753 0.000039 0.213987 0.237923 0.226723 804.28 855.33 1.000
alpha{1,2} 0.197933 0.000134 0.177285 0.221760 0.197176 541.44 651.51 1.000
alpha{3} 3.857770 0.617993 2.422176 5.391641 3.757515 863.86 1120.36 1.000
pinvar{all} 0.038402 0.000217 0.009233 0.066575 0.038096 854.98 1027.96 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 -12531.801681
Model 2: PositiveSelection -12531.801681
Model 0: one-ratio -13037.128452
Model 3: discrete -12461.38368
Model 7: beta -12470.468637
Model 8: beta&w>1 -12464.894345
Model 0 vs 1 1010.653542
Model 2 vs 1 0.0
Model 8 vs 7 11.148583999998664
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
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: gb:KU143801:56-3026|Organism:Zaire_ebolavirus|Strain_Name:Ebola_virus_H.sapiens-wt/SLE/2014/Makona-S33|Protein_Name:nucleprotein|Gene_Symbol:NP)
Pr(w>1) post mean +- SE for w
500 S 0.727 1.303 +- 0.333
501 T 0.599 1.177 +- 0.415
503 G 0.897 1.430 +- 0.213
505 Q 0.515 1.117 +- 0.417
508 N 0.825 1.376 +- 0.277
515 T 0.712 1.288 +- 0.346
520 T 0.748 1.309 +- 0.342
525 T 0.754 1.318 +- 0.330
527 N 0.505 1.103 +- 0.424
539 L 0.756 1.321 +- 0.326
540 T 0.625 1.206 +- 0.397
541 D 0.860 1.404 +- 0.243
550 G 0.618 1.214 +- 0.380
575 S 0.562 1.153 +- 0.414
620 Q 0.601 1.193 +- 0.394
