--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Nov 04 00:51:58 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/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S5/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/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -7424.07         -7444.15
2      -7424.04         -7441.68
--------------------------------------
TOTAL    -7424.05         -7443.54
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/revmuscle/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/revmuscle/S5/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/S5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.426375    0.003662    1.306126    1.543630    1.423657   1383.30   1414.01    1.000
r(A<->C){all}   0.107254    0.000134    0.084813    0.129427    0.107064    980.02   1043.24    1.000
r(A<->G){all}   0.323886    0.000373    0.287849    0.363455    0.323110    604.51    637.98    1.000
r(A<->T){all}   0.078767    0.000061    0.063585    0.093697    0.078639   1035.32   1037.82    1.000
r(C<->G){all}   0.138346    0.000213    0.110366    0.167488    0.137772    984.30   1054.38    1.000
r(C<->T){all}   0.270755    0.000301    0.236655    0.304718    0.270668    880.28    918.88    1.001
r(G<->T){all}   0.080992    0.000084    0.063736    0.098878    0.080549   1102.07   1132.03    1.000
pi(A){all}      0.292442    0.000112    0.271284    0.312944    0.292706   1043.16   1198.88    1.000
pi(C){all}      0.174849    0.000078    0.158255    0.192544    0.174745    980.85   1078.25    1.000
pi(G){all}      0.195289    0.000081    0.178568    0.213335    0.195274    991.53   1051.25    1.000
pi(T){all}      0.337420    0.000127    0.316082    0.359862    0.337484   1115.48   1172.99    1.000
alpha{1,2}      0.883018    0.025913    0.611356    1.205751    0.855502    935.91   1093.07    1.000
alpha{3}        1.509877    0.160454    0.867752    2.316765    1.435413    903.97   1051.19    1.000
pinvar{all}     0.060048    0.001930    0.000026    0.142941    0.051618   1027.63   1084.58    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	-3649.488118
Model 2: PositiveSelection	-3625.008556
Model 0: one-ratio	-3727.832062
Model 3: discrete	-3622.128473
Model 7: beta	-3648.567478
Model 8: beta&w>1	-3621.601279


Model 0 vs 1	156.68788799999948

Model 2 vs 1	48.959123999999974

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)

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

     8 L      0.593         2.778
    36 R      0.872         3.616
    44 I      0.999**       3.996
    46 T      1.000**       3.997
    63 Q      0.845         3.533
    75 Q      0.566         2.697
    78 Y      0.709         3.125
   107 E      0.998**       3.991
   110 C      0.955*        3.863
   126 T      1.000**       3.998
   128 E      0.969*        3.905
   156 K      0.705         3.114
   176 P      0.761         3.283

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: S5_SFBB1)

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

     8 L      0.513         2.543 +- 1.562
    36 R      0.824         3.594 +- 1.331
    44 I      0.999**       4.201 +- 0.684
    46 T      0.999**       4.203 +- 0.680
    63 Q      0.812         3.580 +- 1.377
    75 Q      0.505         2.550 +- 1.596
    78 Y      0.636         2.955 +- 1.558
   107 E      0.997**       4.194 +- 0.699
   110 C      0.941         4.004 +- 0.994
   126 T      1.000**       4.204 +- 0.677
   128 E      0.960*        4.070 +- 0.910
   156 K      0.630         2.939 +- 1.563
   176 P      0.705         3.207 +- 1.524


Model 8 vs 7	53.93239799999992

Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S5_SFBB1)

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

     8 L      0.730         2.730
    21 G      0.620         2.447
    36 R      0.916         3.192
    44 I      0.999**       3.397
    46 T      1.000**       3.398
    63 Q      0.888         3.119
    75 Q      0.685         2.612
    78 Y      0.813         2.937
   107 E      0.998**       3.394
   110 C      0.970*        3.324
   126 T      1.000**       3.399
   128 E      0.978*        3.345
   156 K      0.807         2.918
   176 P      0.848         3.020

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: S5_SFBB1)

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

     8 L      0.648         2.455 +- 1.250
    21 G      0.550         2.190 +- 1.271
    36 R      0.878         3.129 +- 1.032
    44 I      0.999**       3.484 +- 0.676
    46 T      0.999**       3.485 +- 0.674
    63 Q      0.858         3.086 +- 1.092
    75 Q      0.622         2.402 +- 1.292
    78 Y      0.745         2.738 +- 1.204
   107 E      0.997**       3.478 +- 0.685
   110 C      0.960*        3.373 +- 0.829
   126 T      1.000**       3.486 +- 0.673
   128 E      0.971*        3.407 +- 0.789
   156 K      0.737         2.717 +- 1.218
   176 P      0.799         2.906 +- 1.171