--- 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