--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Dec 11 15:24:28 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/pet1/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Paxi_S17_18/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/ADOPS1/pet1/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -13005.99        -13029.65
2     -13005.19        -13025.43
--------------------------------------
TOTAL   -13005.51        -13028.97
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Paxi_S17_18/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/ADOPS1/pet1/Paxi_S17_18/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         3.314020    0.012177    3.107430    3.541277    3.311933   1319.42   1392.99    1.000
r(A<->C){all}   0.129913    0.000097    0.111178    0.149571    0.129551    815.21    836.13    1.000
r(A<->G){all}   0.289550    0.000221    0.261340    0.318448    0.289720    545.21    632.33    1.001
r(A<->T){all}   0.093685    0.000046    0.080302    0.106540    0.093540    743.47    855.97    1.000
r(C<->G){all}   0.144108    0.000136    0.120699    0.167158    0.143902    939.61    984.42    1.000
r(C<->T){all}   0.264744    0.000192    0.240379    0.293945    0.264537    689.11    776.35    1.001
r(G<->T){all}   0.078000    0.000050    0.064308    0.091748    0.077955    742.97    901.38    1.000
pi(A){all}      0.306409    0.000097    0.287048    0.325395    0.306474    766.93    876.17    1.000
pi(C){all}      0.173127    0.000056    0.158969    0.188238    0.173137    600.30    652.91    1.000
pi(G){all}      0.188620    0.000062    0.173871    0.204199    0.188553    813.11    883.35    1.000
pi(T){all}      0.331844    0.000099    0.312849    0.351501    0.331612    879.41    927.65    1.000
alpha{1,2}      1.365841    0.033435    1.044485    1.740269    1.345293   1062.28   1200.18    1.000
alpha{3}        4.358836    0.778390    2.806055    6.140304    4.266587   1343.27   1422.13    1.000
pinvar{all}     0.073339    0.000450    0.030123    0.112874    0.073448    969.40   1117.08    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	-9431.533536
Model 2: PositiveSelection	-9425.946372
Model 0: one-ratio	-9601.348048
Model 3: discrete	-9388.374123
Model 7: beta	-9407.071555
Model 8: beta&w>1	-9388.402901


Model 0 vs 1	339.629023999998

Model 2 vs 1	11.174328000000969

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Paxillaris_S17_SLF10_AB933031)

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

     2 Y      0.760         1.948
     4 F      0.895         2.117
    35 A      0.589         1.734
    55 S      0.893         2.115
    56 L      0.893         2.114
   136 F      0.838         2.046
   139 W      0.551         1.688
   155 F      0.681         1.850
   156 V      0.827         2.031
   272 E      0.679         1.848
   285 A      0.685         1.855

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: 1_Paxillaris_S17_SLF10_AB933031)

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

     2 Y      0.759         2.122 +- 0.660
     4 F      0.890         2.315 +- 0.506
    35 A      0.555         1.815 +- 0.748
    55 S      0.897         2.328 +- 0.494
    56 L      0.895         2.324 +- 0.498
   136 F      0.843         2.248 +- 0.573
   155 F      0.661         1.973 +- 0.720
   156 V      0.832         2.232 +- 0.587
   272 E      0.655         1.963 +- 0.722
   285 A      0.653         1.959 +- 0.721


Model 8 vs 7	37.33730800000194

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Paxillaris_S17_SLF10_AB933031)

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

     2 Y      0.952*        1.678
     4 F      0.989*        1.716
    35 A      0.940         1.667
    38 I      0.615         1.336
    55 S      0.986*        1.712
    56 L      0.987*        1.713
    85 S      0.800         1.524
    87 S      0.762         1.487
    97 A      0.561         1.275
   114 D      0.885         1.611
   117 M      0.824         1.548
   136 F      0.973*        1.699
   139 W      0.925         1.651
   140 F      0.849         1.574
   155 F      0.955*        1.681
   156 V      0.972*        1.698
   199 P      0.853         1.579
   272 E      0.957*        1.684
   285 A      0.956*        1.683

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: 1_Paxillaris_S17_SLF10_AB933031)

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

     2 Y      0.868         1.677 +- 0.549
     4 F      0.955*        1.756 +- 0.489
    35 A      0.830         1.627 +- 0.552
    55 S      0.947         1.752 +- 0.497
    56 L      0.949         1.753 +- 0.495
    85 S      0.591         1.342 +- 0.573
    87 S      0.523         1.250 +- 0.522
   114 D      0.729         1.513 +- 0.583
   117 M      0.617         1.369 +- 0.570
   136 F      0.914         1.722 +- 0.520
   139 W      0.786         1.567 +- 0.560
   140 F      0.656         1.416 +- 0.575
   155 F      0.865         1.667 +- 0.541
   156 V      0.911         1.720 +- 0.522
   199 P      0.675         1.449 +- 0.586
   272 E      0.870         1.671 +- 0.538
   285 A      0.867         1.666 +- 0.540