--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Oct 18 17:14:11 WEST 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=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/Ebola_B1/GP/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/Ebola_B1/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/GP/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/ADOPS/Ebola_B1/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -14211.37        -14260.32
2     -14212.59        -14258.57
--------------------------------------
TOTAL   -14211.80        -14259.79
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/Ebola_B1/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/Ebola_B1/GP/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/ADOPS/Ebola_B1/GP/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         6.769741    0.223639    5.878072    7.703055    6.760136    112.55    196.76    1.032
r(A<->C){all}   0.180604    0.000184    0.154130    0.207151    0.180306    647.29    798.97    1.001
r(A<->G){all}   0.284865    0.000276    0.252939    0.316466    0.284523    821.49    824.54    1.000
r(A<->T){all}   0.086121    0.000117    0.064931    0.106871    0.085861    850.61    901.02    1.000
r(C<->G){all}   0.076715    0.000140    0.053142    0.099075    0.076788    888.72    955.02    1.000
r(C<->T){all}   0.308673    0.000300    0.274672    0.342662    0.308792    801.88    829.46    1.000
r(G<->T){all}   0.063021    0.000120    0.042877    0.085240    0.062410    978.78    998.17    1.004
pi(A){all}      0.305995    0.000040    0.294191    0.318164    0.306121    859.90    888.24    1.000
pi(C){all}      0.267787    0.000037    0.255864    0.279460    0.267683    755.48    775.00    1.001
pi(G){all}      0.208429    0.000034    0.196665    0.219257    0.208453    812.30    884.11    1.001
pi(T){all}      0.217790    0.000033    0.206325    0.228807    0.217742    655.33    836.43    1.000
alpha{1,2}      0.538401    0.001372    0.466692    0.610149    0.537607    928.35   1018.79    1.001
alpha{3}        5.611367    1.317641    3.585960    7.798787    5.496119   1328.00   1366.13    1.000
pinvar{all}     0.009517    0.000048    0.000017    0.022410    0.008146   1189.47   1295.10    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	-7414.394937
Model 2: PositiveSelection	-7414.394937
Model 0: one-ratio	-7556.998822
Model 3: discrete	-7371.991199
Model 7: beta	-7383.399332
Model 8: beta&w>1	-7375.137864


Model 0 vs 1	285.2077699999991

Model 2 vs 1	0.0

Model 8 vs 7	16.52293599999939

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:KU174140|Organism:Zaire ebolavirus|Strain Name:Ebola virus/H.sapiens-rec/COD/1976/Yambuku-Mayinga-eGFP-MARV_GP|Protein Name:GP|Gene Symbol:GP)

            Pr(w>1)     post mean +- SE for w