--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Nov 03 10:30:16 WET 2017
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=
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Srevisao1/S3_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S3_16Malus/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/Srevisao1/S3_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -8447.31         -8465.58
2      -8447.21         -8468.32
--------------------------------------
TOTAL    -8447.26         -8467.69
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao1/S3_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao1/S3_16Malus/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/Srevisao1/S3_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.451176    0.003050    1.344876    1.560936    1.449863   1501.00   1501.00    1.000
r(A<->C){all}   0.118276    0.000120    0.098448    0.141654    0.117703   1034.30   1036.06    1.000
r(A<->G){all}   0.297621    0.000297    0.263423    0.330894    0.297991    975.44   1009.02    1.001
r(A<->T){all}   0.078298    0.000054    0.064985    0.093007    0.078071    973.82   1109.33    1.000
r(C<->G){all}   0.146669    0.000196    0.120430    0.174387    0.146111    784.35    895.74    1.000
r(C<->T){all}   0.282057    0.000282    0.250558    0.315311    0.281764    976.12   1033.75    1.000
r(G<->T){all}   0.077079    0.000065    0.062843    0.094322    0.076976   1053.62   1154.10    1.000
pi(A){all}      0.300031    0.000110    0.280502    0.321041    0.299978   1067.28   1090.79    1.003
pi(C){all}      0.164201    0.000066    0.148123    0.180273    0.164111    979.03   1071.05    1.001
pi(G){all}      0.188529    0.000075    0.172145    0.205610    0.188404    748.55   1027.10    1.001
pi(T){all}      0.347238    0.000122    0.326076    0.368416    0.347348    419.04    711.57    1.000
alpha{1,2}      0.912984    0.016256    0.701384    1.187658    0.894278   1181.69   1300.95    1.000
alpha{3}        1.635071    0.122249    1.061276    2.330674    1.586063   1236.21   1311.76    1.000
pinvar{all}     0.036065    0.000867    0.000006    0.093456    0.028958   1252.37   1367.10    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	-5671.082625
Model 2: PositiveSelection	-5628.688889
Model 0: one-ratio	-5792.824008
Model 3: discrete	-5627.467661
Model 7: beta	-5675.259133
Model 8: beta&w>1	-5627.044887


Model 0 vs 1	243.48276599999917

Model 2 vs 1	84.78747199999998

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_SFBB1)

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

    42 N      0.990**       4.384
    48 R      1.000**       4.417
    52 P      0.992**       4.391
    81 L      0.998**       4.411
    86 F      0.523         2.786
    88 E      0.971*        4.318
   128 R      0.924         4.159
   136 I      1.000**       4.417
   138 T      0.997**       4.409
   155 Q      0.614         3.100
   184 T      0.604         3.066
   202 C      0.825         3.820
   218 T      1.000**       4.418
   220 E      0.995**       4.400

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_SFBB1)

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

    42 N      0.987*        4.510 +- 0.678
    48 R      1.000**       4.559 +- 0.548
    52 P      0.990*        4.523 +- 0.649
    81 L      0.997**       4.551 +- 0.574
    88 E      0.966*        4.439 +- 0.840
   128 R      0.897         4.171 +- 1.188
   136 I      1.000**       4.559 +- 0.549
   138 T      0.997**       4.549 +- 0.579
   155 Q      0.570         2.994 +- 1.779
   184 T      0.548         2.896 +- 1.765
   202 C      0.776         3.723 +- 1.533
   218 T      1.000**       4.560 +- 0.545
   220 E      0.994**       4.537 +- 0.612


Model 8 vs 7	96.4284919999991

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_SFBB1)

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

    42 N      0.995**       3.867
    48 R      1.000**       3.881
    52 P      0.996**       3.869
    81 L      0.999**       3.878
    86 F      0.716         3.037
    88 E      0.981*        3.824
   128 R      0.962*        3.768
   136 I      1.000**       3.881
   138 T      0.999**       3.877
   155 Q      0.720         3.035
   184 T      0.746         3.118
   202 C      0.908         3.608
   218 T      1.000**       3.881
   220 E      0.997**       3.873

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_SFBB1)

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

    42 N      0.994**       3.972 +- 0.583
    48 R      1.000**       3.991 +- 0.536
    52 P      0.995**       3.976 +- 0.576
    81 L      0.999**       3.987 +- 0.547
    86 F      0.653         2.853 +- 1.483
    88 E      0.978*        3.924 +- 0.698
   128 R      0.950         3.828 +- 0.848
   136 I      1.000**       3.991 +- 0.536
   138 T      0.998**       3.986 +- 0.549
   155 Q      0.678         2.961 +- 1.513
   184 T      0.695         3.001 +- 1.475
   202 C      0.882         3.605 +- 1.109
   218 T      1.000**       3.991 +- 0.535
   220 E      0.997**       3.981 +- 0.562