--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Dec 07 17:03:05 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/408/Sudx-PF/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/408/Sudx-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PF/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/408/Sudx-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -10162.39        -10178.07
2     -10162.07        -10181.03
--------------------------------------
TOTAL   -10162.22        -10180.39
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/408/Sudx-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/408/Sudx-PF/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/408/Sudx-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.282685    0.003829    1.156749    1.399114    1.282120   1305.40   1335.90    1.000
r(A<->C){all}   0.093834    0.000095    0.074435    0.112230    0.093473    910.57   1055.51    1.000
r(A<->G){all}   0.284124    0.000323    0.251081    0.321038    0.283889    814.19    877.67    1.000
r(A<->T){all}   0.074967    0.000143    0.052488    0.098995    0.074411    847.45    906.80    1.000
r(C<->G){all}   0.036270    0.000029    0.025787    0.046738    0.036085   1132.84   1208.66    1.001
r(C<->T){all}   0.440233    0.000463    0.401128    0.485242    0.440446    680.85    753.00    1.001
r(G<->T){all}   0.070573    0.000085    0.053926    0.088617    0.070417    938.16   1021.29    1.000
pi(A){all}      0.235559    0.000056    0.220501    0.249810    0.235501    889.76    917.09    1.000
pi(C){all}      0.283427    0.000057    0.269262    0.298450    0.283470   1227.00   1256.59    1.000
pi(G){all}      0.296065    0.000063    0.280147    0.311463    0.296101   1153.59   1180.26    1.000
pi(T){all}      0.184949    0.000040    0.172527    0.197262    0.184995   1146.82   1216.24    1.001
alpha{1,2}      0.123512    0.000054    0.109785    0.138680    0.123339   1319.32   1410.16    1.001
alpha{3}        5.262866    1.117355    3.449518    7.362469    5.143597   1224.87   1287.95    1.000
pinvar{all}     0.375920    0.000475    0.335923    0.419581    0.376729   1242.68   1290.82    1.001
------------------------------------------------------------------------------------------------------
* 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	-9281.48237
Model 2: PositiveSelection	-9281.482466
Model 0: one-ratio	-9355.132281
Model 3: discrete	-9266.787676
Model 7: beta	-9268.495154
Model 8: beta&w>1	-9264.543014


Model 0 vs 1	147.29982200000086

Model 2 vs 1	1.919999995152466E-4

Model 8 vs 7	7.904279999998835

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_Sudx-PF)

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

    21 T      0.716         1.154
   187 A      0.944         1.448
   324 P      0.981*        1.494

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_Sudx-PF)

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

    21 T      0.794         1.326 +- 0.409
   185 P      0.645         1.155 +- 0.514
   187 A      0.912         1.446 +- 0.299
   233 G      0.691         1.207 +- 0.495
   322 G      0.657         1.168 +- 0.509
   323 P      0.650         1.161 +- 0.512
   324 P      0.956*        1.487 +- 0.244