--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 10:18:49 WET 2016
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=/opt/ADOPS/423/Trpm-PF/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/423/Trpm-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/423/Trpm-PF/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/ADOPS/423/Trpm-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1     -18080.58        -18096.84
2     -18080.86        -18094.26
--------------------------------------
TOTAL   -18080.71        -18096.22
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/423/Trpm-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/423/Trpm-PF/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/ADOPS/423/Trpm-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.767120    0.000901    0.710947    0.828617    0.766397   1481.43   1491.21    1.000
r(A<->C){all}   0.082104    0.000062    0.066556    0.096896    0.081836   1025.05   1102.92    1.001
r(A<->G){all}   0.246210    0.000198    0.218636    0.272984    0.245662    678.15    727.13    1.000
r(A<->T){all}   0.121983    0.000153    0.097826    0.146168    0.121470    838.12    882.32    1.000
r(C<->G){all}   0.072134    0.000034    0.060871    0.083525    0.071871   1047.26   1174.89    1.000
r(C<->T){all}   0.419281    0.000282    0.387191    0.451016    0.419401    881.85    889.04    1.000
r(G<->T){all}   0.058287    0.000050    0.044463    0.071728    0.058044   1007.55   1079.22    1.000
pi(A){all}      0.218603    0.000025    0.209795    0.228892    0.218457   1009.55   1048.15    1.000
pi(C){all}      0.309393    0.000031    0.299456    0.320962    0.309337   1143.36   1164.67    1.000
pi(G){all}      0.288916    0.000030    0.278165    0.299566    0.289076    929.37   1065.02    1.001
pi(T){all}      0.183088    0.000021    0.174175    0.191637    0.183103    916.79    930.00    1.000
alpha{1,2}      0.121512    0.000049    0.108425    0.135335    0.121372   1501.00   1501.00    1.001
alpha{3}        6.159051    1.406847    4.022636    8.593728    6.039342   1372.47   1413.70    1.000
pinvar{all}     0.500490    0.000260    0.470088    0.531991    0.500695   1443.76   1472.38    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	-16413.764536
Model 2: PositiveSelection	-16413.76472
Model 0: one-ratio	-16554.752649
Model 3: discrete	-16398.454008
Model 7: beta	-16410.548868
Model 8: beta&w>1	-16398.604114


Model 0 vs 1	281.97622599999886

Model 2 vs 1	3.680000008898787E-4

Model 8 vs 7	23.889508000000205

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

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

    36 T      0.816         1.954
  1040 G      0.939         2.213
  1051 S      0.997**       2.334
  1053 T      0.942         2.220
  1324 G      0.762         1.841
  1542 I      0.987*        2.314
  1547 A      0.969*        2.276

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: D_melanogaster_Trpm-PF)

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

    36 T      0.869         1.382 +- 0.333
  1040 G      0.919         1.434 +- 0.254
  1044 T      0.605         1.068 +- 0.565
  1045 V      0.579         1.042 +- 0.568
  1050 T      0.626         1.093 +- 0.557
  1051 S      0.972*        1.482 +- 0.152
  1052 T      0.551         1.008 +- 0.575
  1053 T      0.919         1.434 +- 0.254
  1058 S      0.629         1.132 +- 0.503
  1324 G      0.850         1.362 +- 0.354
  1325 P      0.702         1.208 +- 0.474
  1339 V      0.744         1.252 +- 0.448
  1542 I      0.954*        1.466 +- 0.190
  1547 A      0.938         1.451 +- 0.224
  1828 T      0.511         0.953 +- 0.591
  1905 Q      0.712         1.219 +- 0.466