--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sat Nov 19 01:15:13 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/274/Hsc70-5-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/274/Hsc70-5-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/274/Hsc70-5-PA/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/274/Hsc70-5-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -6762.67         -6778.60
2      -6762.83         -6778.26
--------------------------------------
TOTAL    -6762.75         -6778.44
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/274/Hsc70-5-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/274/Hsc70-5-PA/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/274/Hsc70-5-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.142365    0.004460    1.018508    1.279946    1.141402   1261.32   1367.34    1.001
r(A<->C){all}   0.063453    0.000106    0.045425    0.085048    0.063129   1075.06   1109.57    1.000
r(A<->G){all}   0.239397    0.000515    0.195501    0.285261    0.238781    837.57    890.22    1.001
r(A<->T){all}   0.108232    0.000373    0.072535    0.148774    0.106861    811.58    850.21    1.000
r(C<->G){all}   0.029086    0.000030    0.018373    0.039906    0.028819   1075.69   1189.47    1.001
r(C<->T){all}   0.486673    0.000713    0.432994    0.536510    0.485808    798.22    858.80    1.000
r(G<->T){all}   0.073160    0.000124    0.052147    0.095207    0.072566    967.06   1054.43    1.001
pi(A){all}      0.220938    0.000077    0.204258    0.237830    0.220798    969.31   1098.05    1.000
pi(C){all}      0.295086    0.000084    0.277393    0.312273    0.295085    966.74   1102.95    1.000
pi(G){all}      0.289673    0.000094    0.271855    0.308754    0.289796   1177.93   1245.48    1.000
pi(T){all}      0.194302    0.000059    0.178792    0.208944    0.194406   1123.97   1131.86    1.000
alpha{1,2}      0.084933    0.000049    0.071485    0.098219    0.084758   1369.91   1431.08    1.000
alpha{3}        4.574438    1.022920    2.774277    6.579811    4.484073   1487.34   1494.17    1.000
pinvar{all}     0.358231    0.000744    0.304625    0.411738    0.358489   1091.67   1247.34    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	-6298.787654
Model 2: PositiveSelection	-6298.787654
Model 0: one-ratio	-6338.704008
Model 3: discrete	-6288.661124
Model 7: beta	-6292.126465
Model 8: beta&w>1	-6289.117973


Model 0 vs 1	79.83270799999991

Model 2 vs 1	0.0

Model 8 vs 7	6.016983999999866

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_Hsc70-5-PA)

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

   660 N      0.995**       0.996
   661 A      0.721         0.760

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_Hsc70-5-PA)

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

   660 N      0.820         1.431 +- 0.511
   661 A      0.640         1.214 +- 0.661
   662 G      0.581         1.113 +- 0.721