--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Oct 31 19:37:21 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/128/CG34135-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/128/CG34135-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/128/CG34135-PC/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/128/CG34135-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1397.97         -1416.91
2      -1397.73         -1415.30
--------------------------------------
TOTAL    -1397.84         -1416.40
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/128/CG34135-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/128/CG34135-PC/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/128/CG34135-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.576089    0.040436    1.181268    1.948034    1.559422   1152.11   1276.67    1.000
r(A<->C){all}   0.098913    0.001038    0.039216    0.162479    0.096602    737.94    823.77    1.000
r(A<->G){all}   0.221962    0.002158    0.133351    0.314957    0.219489    574.55    667.95    1.000
r(A<->T){all}   0.171376    0.002830    0.068286    0.269458    0.169705    554.55    569.91    1.000
r(C<->G){all}   0.051327    0.000308    0.020564    0.087596    0.049935    876.27   1066.24    1.000
r(C<->T){all}   0.360973    0.002830    0.260173    0.464100    0.360128    679.42    752.86    1.000
r(G<->T){all}   0.095450    0.000855    0.038454    0.152650    0.092364    910.66    971.12    1.000
pi(A){all}      0.173138    0.000282    0.141803    0.206391    0.172728   1294.15   1305.32    1.001
pi(C){all}      0.314535    0.000428    0.273723    0.354166    0.314167   1154.10   1223.84    1.000
pi(G){all}      0.278350    0.000424    0.240417    0.321302    0.277967   1193.27   1334.14    1.000
pi(T){all}      0.233977    0.000363    0.197657    0.272579    0.233701   1007.43   1022.75    1.000
alpha{1,2}      0.074869    0.000116    0.054041    0.095729    0.074391   1404.65   1452.82    1.000
alpha{3}        2.588000    0.626118    1.257271    4.189710    2.460149   1184.46   1280.65    1.000
pinvar{all}     0.384506    0.002871    0.281405    0.488287    0.385063   1309.37   1376.30    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	-1271.471055
Model 2: PositiveSelection	-1271.469716
Model 0: one-ratio	-1271.53949
Model 3: discrete	-1271.469716
Model 7: beta	-1271.469025
Model 8: beta&w>1	-1271.470364


Model 0 vs 1	0.13686999999981708

Model 2 vs 1	0.0026779999998325366

Model 8 vs 7	0.0026779999998325366