--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 22 00:46:47 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/3/AcCoAS-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

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

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -5584.69         -5600.22
2      -5584.55         -5600.60
--------------------------------------
TOTAL    -5584.62         -5600.43
--------------------------------------


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

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.288775    0.006393    1.132147    1.444876    1.288399   1182.85   1341.93    1.000
r(A<->C){all}   0.100231    0.000231    0.072981    0.130568    0.099263    952.89   1073.81    1.000
r(A<->G){all}   0.250775    0.000588    0.206710    0.302253    0.250154   1074.14   1083.19    1.000
r(A<->T){all}   0.110192    0.000407    0.072614    0.151121    0.109403   1016.51   1114.87    1.000
r(C<->G){all}   0.049593    0.000066    0.033869    0.065552    0.049290    978.57   1065.53    1.000
r(C<->T){all}   0.419698    0.000749    0.366935    0.473918    0.419220    774.89    901.43    1.000
r(G<->T){all}   0.069511    0.000135    0.048232    0.093220    0.069159   1034.08   1155.61    1.001
pi(A){all}      0.197824    0.000092    0.178112    0.216090    0.197456   1001.50   1037.98    1.000
pi(C){all}      0.292759    0.000108    0.272884    0.312800    0.292619   1008.47   1057.27    1.000
pi(G){all}      0.300240    0.000120    0.278780    0.321337    0.300212    950.20   1025.58    1.000
pi(T){all}      0.209178    0.000088    0.189677    0.227180    0.208859   1043.90   1095.76    1.000
alpha{1,2}      0.102111    0.000056    0.087636    0.116346    0.101816   1190.71   1213.01    1.000
alpha{3}        4.341082    0.924845    2.662822    6.215105    4.226608   1098.21   1299.61    1.000
pinvar{all}     0.359356    0.000846    0.303228    0.417332    0.359921   1135.31   1318.15    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	-5139.879125
Model 2: PositiveSelection	-5139.879125
Model 0: one-ratio	-5163.544282
Model 3: discrete	-5138.1288
Model 7: beta	-5144.745954
Model 8: beta&w>1	-5138.502955


Model 0 vs 1	47.33031399999891

Model 2 vs 1	0.0

Model 8 vs 7	12.485998000000109

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_AcCoAS-PB)

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

   276 Y      1.000**       1.165

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: D_melanogaster_AcCoAS-PB)

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

   276 Y      0.661         1.500 +- 0.921