--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 19:06:12 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/442/Zasp52-PX/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/442/Zasp52-PX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PX/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/442/Zasp52-PX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -17492.12        -17504.38
2     -17491.51        -17505.99
--------------------------------------
TOTAL   -17491.77        -17505.48
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/442/Zasp52-PX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/442/Zasp52-PX/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/442/Zasp52-PX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.526557    0.000550    0.478922    0.570193    0.526054   1062.77   1199.39    1.000
r(A<->C){all}   0.074316    0.000066    0.058248    0.089894    0.074127   1045.79   1115.35    1.001
r(A<->G){all}   0.227114    0.000219    0.198812    0.256377    0.226743    852.69    921.04    1.000
r(A<->T){all}   0.178340    0.000238    0.147499    0.207461    0.177984    987.49   1072.11    1.000
r(C<->G){all}   0.057667    0.000036    0.046759    0.069950    0.057427   1190.73   1209.92    1.000
r(C<->T){all}   0.383968    0.000338    0.348981    0.419341    0.384073    894.89    935.04    1.000
r(G<->T){all}   0.078595    0.000088    0.060207    0.096855    0.078452   1044.99   1105.94    1.000
pi(A){all}      0.233437    0.000025    0.224114    0.243428    0.233430   1004.00   1070.69    1.000
pi(C){all}      0.334129    0.000030    0.323779    0.345398    0.334045   1118.44   1123.70    1.000
pi(G){all}      0.263307    0.000027    0.252902    0.273093    0.263317   1161.91   1196.19    1.000
pi(T){all}      0.169128    0.000018    0.160294    0.176869    0.169133   1098.34   1115.85    1.000
alpha{1,2}      0.150241    0.000175    0.123181    0.175005    0.149525   1336.99   1376.68    1.000
alpha{3}        5.882425    1.631466    3.586137    8.445575    5.717311   1293.15   1341.47    1.000
pinvar{all}     0.399978    0.000693    0.348814    0.452827    0.400995   1259.90   1309.50    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	-15475.649296
Model 2: PositiveSelection	-15475.649296
Model 0: one-ratio	-15653.204243
Model 3: discrete	-15473.799784
Model 7: beta	-15475.812597
Model 8: beta&w>1	-15473.833531


Model 0 vs 1	355.1098940000011

Model 2 vs 1	0.0

Model 8 vs 7	3.9581319999997504