--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Tue Nov 07 11:34:11 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/S2novarevisao/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/Muscle/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/S2novarevisao/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7958.92         -7975.10
2      -7958.46         -7975.31
--------------------------------------
TOTAL    -7958.66         -7975.21
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/S2novarevisao/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/S2novarevisao/Muscle/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/S2novarevisao/Muscle/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.408772    0.003127    1.299026    1.515676    1.407621   1501.00   1501.00    1.000
r(A<->C){all}   0.100019    0.000115    0.079134    0.120578    0.099491   1084.52   1093.45    1.001
r(A<->G){all}   0.297995    0.000327    0.263438    0.332558    0.297953    725.85    856.74    1.000
r(A<->T){all}   0.072872    0.000050    0.059291    0.086684    0.072712    977.18   1036.35    1.000
r(C<->G){all}   0.156261    0.000217    0.128730    0.185490    0.156025    773.98    881.89    1.000
r(C<->T){all}   0.288952    0.000317    0.255188    0.323698    0.288482    850.16    879.01    1.000
r(G<->T){all}   0.083901    0.000079    0.066795    0.101750    0.083641    930.48    933.69    1.000
pi(A){all}      0.300246    0.000116    0.280133    0.322124    0.300162    870.76    979.08    1.001
pi(C){all}      0.169117    0.000070    0.152474    0.184963    0.169014    838.18    912.91    1.000
pi(G){all}      0.190385    0.000079    0.172544    0.207438    0.190125   1018.29   1114.43    1.000
pi(T){all}      0.340253    0.000136    0.315430    0.361002    0.340425    575.67    758.53    1.000
alpha{1,2}      0.806107    0.012028    0.626842    1.043898    0.792194    925.20   1213.10    1.000
alpha{3}        1.787298    0.149750    1.119227    2.559372    1.735916   1204.48   1204.93    1.000
pinvar{all}     0.032112    0.000742    0.000005    0.085947    0.024958   1248.43   1311.74    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	-5420.915317
Model 2: PositiveSelection	-5390.19306
Model 0: one-ratio	-5530.65893
Model 3: discrete	-5387.642397
Model 7: beta	-5426.083543
Model 8: beta&w>1	-5388.163064


Model 0 vs 1	219.48722599999928

Model 2 vs 1	61.44451400000071

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S2_SFBB1)

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

    10 M      0.826         3.086
    27 N      0.986*        3.489
    33 R      0.999**       3.524
    37 P      0.670         2.692
    66 L      0.935         3.360
    73 E      0.997**       3.518
    85 L      0.756         2.910
    86 A      0.563         2.422
   113 S      0.634         2.601
   114 R      0.929         3.346
   122 I      0.999**       3.522
   124 T      0.999**       3.523
   141 Q      0.715         2.805
   153 Q      0.529         2.336
   170 T      0.809         3.044
   188 C      0.561         2.418
   204 T      0.999**       3.522
   206 E      0.975*        3.462
   257 T      0.648         2.636

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: S2_SFBB1)

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

    10 M      0.784         3.068 +- 1.137
    27 N      0.982*        3.611 +- 0.538
    33 R      0.999**       3.659 +- 0.413
    37 P      0.605         2.578 +- 1.303
    66 L      0.917         3.434 +- 0.826
    73 E      0.997**       3.653 +- 0.434
    85 L      0.697         2.825 +- 1.240
   113 S      0.575         2.505 +- 1.323
   114 R      0.908         3.407 +- 0.854
   122 I      0.999**       3.658 +- 0.419
   124 T      0.999**       3.659 +- 0.414
   141 Q      0.666         2.754 +- 1.282
   170 T      0.768         3.028 +- 1.165
   204 T      0.999**       3.657 +- 0.419
   206 E      0.969*        3.576 +- 0.612
   257 T      0.574         2.485 +- 1.304


Model 8 vs 7	75.84095799999886

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S2_SFBB1)

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

    10 M      0.927         2.798
    27 N      0.995**       2.939
    33 R      1.000**       2.948
    37 P      0.859         2.655
    66 L      0.974*        2.894
    71 F      0.585         2.082
    73 E      0.999**       2.946
    75 G      0.698         2.316
    85 L      0.902         2.746
    86 A      0.795         2.520
   113 S      0.807         2.542
   114 R      0.973*        2.892
   122 I      0.999**       2.948
   124 T      1.000**       2.948
   141 Q      0.852         2.638
   153 Q      0.738         2.396
   156 Y      0.607         2.130
   160 A      0.510         1.923
   170 T      0.912         2.766
   185 E      0.669         2.258
   188 C      0.785         2.498
   204 T      0.999**       2.948
   206 E      0.990*        2.928
   257 T      0.858         2.653

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: S2_SFBB1)

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

    10 M      0.919         2.645 +- 0.698
    27 N      0.994**       2.823 +- 0.512
    33 R      1.000**       2.836 +- 0.494
    37 P      0.845         2.466 +- 0.798
    66 L      0.970*        2.767 +- 0.583
    71 F      0.637         1.993 +- 0.902
    73 E      0.998**       2.834 +- 0.498
    75 G      0.713         2.163 +- 0.899
    85 L      0.887         2.566 +- 0.743
    86 A      0.787         2.331 +- 0.854
    98 G      0.554         1.822 +- 0.959
   113 S      0.805         2.380 +- 0.858
   114 R      0.968*        2.762 +- 0.587
   122 I      0.999**       2.835 +- 0.495
   124 T      1.000**       2.836 +- 0.494
   141 Q      0.849         2.487 +- 0.816
   153 Q      0.747         2.248 +- 0.900
   156 Y      0.653         2.025 +- 0.895
   160 A      0.589         1.885 +- 0.898
   170 T      0.906         2.616 +- 0.725
   185 E      0.688         2.098 +- 0.886
   188 C      0.780         2.316 +- 0.864
   204 T      0.999**       2.835 +- 0.495
   206 E      0.989*        2.811 +- 0.530
   257 T      0.837         2.443 +- 0.800