--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 25 14:24:12 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
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/ADOPS/1/14-3-3zeta-PG/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/1/14-3-3zeta-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/14-3-3zeta-PG/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/1/14-3-3zeta-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1544.40         -1562.83
2      -1544.56         -1563.72
--------------------------------------
TOTAL    -1544.48         -1563.37
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/1/14-3-3zeta-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/14-3-3zeta-PG/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/1/14-3-3zeta-PG/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.247920    0.001647    0.176359    0.333366    0.244050   1307.41   1310.60    1.000
r(A<->C){all}   0.111095    0.001122    0.050567    0.178397    0.108058    747.82    835.04    1.000
r(A<->G){all}   0.152878    0.001703    0.077245    0.231470    0.148975    860.48   1021.09    1.000
r(A<->T){all}   0.067466    0.001098    0.012128    0.133970    0.062763    572.59    693.46    1.000
r(C<->G){all}   0.061421    0.000641    0.016602    0.111196    0.058105    899.13   1064.58    1.000
r(C<->T){all}   0.558366    0.004760    0.430141    0.696077    0.558382    677.21    764.72    1.000
r(G<->T){all}   0.048773    0.000730    0.003535    0.099599    0.044829    649.11    806.42    1.001
pi(A){all}      0.285953    0.000252    0.253916    0.314870    0.285640   1172.42   1266.40    1.003
pi(C){all}      0.261314    0.000221    0.232901    0.290045    0.260857   1057.87   1220.34    1.000
pi(G){all}      0.258237    0.000240    0.228554    0.287916    0.258559   1103.28   1177.05    1.001
pi(T){all}      0.194496    0.000198    0.166689    0.220516    0.194117   1180.49   1220.57    1.000
alpha{1,2}      0.056370    0.001757    0.000143    0.134510    0.048662   1226.83   1234.60    1.000
alpha{3}        2.077090    0.654349    0.694719    3.637498    1.954483   1378.89   1439.94    1.000
pinvar{all}     0.475676    0.008692    0.280469    0.634387    0.488729   1139.60   1235.02    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	-1451.36118
Model 2: PositiveSelection	-1451.36118
Model 0: one-ratio	-1458.92382
Model 3: discrete	-1451.332921
Model 7: beta	-1451.333746
Model 8: beta&w>1	-1451.361179


Model 0 vs 1	15.125279999999748

Model 2 vs 1	0.0

Model 8 vs 7	0.054865999999947235