--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Nov 04 02:14:22 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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S9/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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8659.11         -8678.27
2      -8660.05         -8685.87
--------------------------------------
TOTAL    -8659.47         -8685.18
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S9/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/revmuscle/S9/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.558293    0.003613    1.446847    1.677442    1.556226   1416.88   1458.94    1.000
r(A<->C){all}   0.107070    0.000111    0.087674    0.128343    0.106703    832.61    970.19    1.000
r(A<->G){all}   0.296124    0.000334    0.260845    0.332910    0.295945    595.85    769.66    1.000
r(A<->T){all}   0.075597    0.000052    0.061279    0.088632    0.075333   1160.76   1161.35    1.001
r(C<->G){all}   0.168509    0.000213    0.138106    0.195547    0.168272    745.59    938.09    1.000
r(C<->T){all}   0.278580    0.000299    0.245780    0.311627    0.278315    831.29    879.13    1.000
r(G<->T){all}   0.074119    0.000066    0.058141    0.089658    0.073852    973.41   1124.51    1.000
pi(A){all}      0.303728    0.000123    0.283066    0.325835    0.303460    906.22    929.80    1.000
pi(C){all}      0.169499    0.000071    0.153626    0.186668    0.169281   1059.32   1085.98    1.001
pi(G){all}      0.186026    0.000080    0.168376    0.202547    0.185892    766.40    883.99    1.000
pi(T){all}      0.340747    0.000136    0.318077    0.363741    0.340559    892.74    897.73    1.001
alpha{1,2}      0.850847    0.012325    0.651088    1.081700    0.838039   1051.10   1236.90    1.000
alpha{3}        1.624522    0.108844    1.092232    2.319610    1.580005   1306.98   1316.63    1.000
pinvar{all}     0.033997    0.000743    0.000004    0.088343    0.027645   1295.71   1299.51    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	-5488.987427
Model 2: PositiveSelection	-5451.403633
Model 0: one-ratio	-5622.903996
Model 3: discrete	-5449.402515
Model 7: beta	-5495.653586
Model 8: beta&w>1	-5451.373108


Model 0 vs 1	267.83313799999996

Model 2 vs 1	75.16758800000025

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)

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

    14 T      0.986*        3.484
    20 N      1.000**       3.519
    24 Q      0.989*        3.491
    53 L      0.955*        3.407
    58 Y      0.724         2.823
    60 L      0.991**       3.498
    62 L      0.784         2.975
    73 A      0.729         2.836
    99 K      0.970*        3.443
   107 V      0.999**       3.517
   109 R      1.000**       3.518
   138 R      0.597         2.505
   155 T      0.785         2.977
   170 K      0.964*        3.430
   173 S      0.784         2.974
   189 T      1.000**       3.519
   191 A      0.978*        3.464
   219 K      0.757         2.908
   242 E      0.511         2.287

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: S3_S9_AB539854_MdFBX11)

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

    14 T      0.980*        3.555 +- 0.485
    20 N      1.000**       3.608 +- 0.330
    24 Q      0.985*        3.569 +- 0.453
    53 L      0.940         3.450 +- 0.692
    58 Y      0.653         2.677 +- 1.243
    60 L      0.989*        3.581 +- 0.422
    62 L      0.728         2.885 +- 1.180
    73 A      0.661         2.702 +- 1.240
    99 K      0.960*        3.502 +- 0.603
   107 V      0.999**       3.606 +- 0.337
   109 R      0.999**       3.607 +- 0.332
   138 R      0.529         2.361 +- 1.303
   155 T      0.730         2.891 +- 1.179
   170 K      0.951*        3.478 +- 0.643
   173 S      0.728         2.884 +- 1.180
   189 T      1.000**       3.609 +- 0.327
   191 A      0.971*        3.533 +- 0.541
   219 K      0.695         2.793 +- 1.213


Model 8 vs 7	88.56095600000117

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S3_S9_AB539854_MdFBX11)

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

    14 T      0.994**       2.991
    20 N      1.000**       3.003
    24 Q      0.995**       2.992
    53 L      0.979*        2.960
    58 Y      0.876         2.742
    60 L      0.995**       2.993
    62 L      0.893         2.777
    72 T      0.533         2.003
    73 A      0.872         2.731
    85 R      0.589         2.113
    99 K      0.986*        2.973
   107 V      1.000**       3.002
   109 R      1.000**       3.003
   126 Q      0.658         2.267
   138 R      0.762         2.493
   141 Y      0.635         2.229
   155 T      0.890         2.769
   170 K      0.985*        2.972
   173 S      0.898         2.787
   189 T      1.000**       3.003
   191 A      0.990*        2.981
   214 R      0.621         2.193
   219 K      0.881         2.751
   239 R      0.639         2.228
   242 E      0.734         2.438

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: S3_S9_AB539854_MdFBX11)

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

    14 T      0.993**       2.771 +- 0.481
    20 N      1.000**       2.786 +- 0.460
    24 Q      0.994**       2.773 +- 0.480
    53 L      0.977*        2.736 +- 0.530
    58 Y      0.874         2.492 +- 0.722
    60 L      0.995**       2.775 +- 0.478
    62 L      0.893         2.544 +- 0.708
    72 T      0.629         1.966 +- 0.893
    73 A      0.871         2.491 +- 0.735
    85 R      0.651         2.022 +- 0.923
    99 K      0.985*        2.752 +- 0.509
   107 V      0.999**       2.785 +- 0.462
   109 R      1.000**       2.785 +- 0.461
   126 Q      0.705         2.132 +- 0.893
   138 R      0.784         2.304 +- 0.843
   141 Y      0.704         2.119 +- 0.855
   155 T      0.890         2.539 +- 0.717
   170 K      0.983*        2.748 +- 0.512
   173 S      0.897         2.553 +- 0.700
   189 T      1.000**       2.786 +- 0.460
   191 A      0.989*        2.762 +- 0.496
   214 R      0.686         2.082 +- 0.875
   219 K      0.880         2.512 +- 0.724
   239 R      0.693         2.105 +- 0.892
   242 E      0.764         2.248 +- 0.833