--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Jan 23 17:03:42 GMT 2020
codeml.models=0 1 2 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/opt/mrbayes_3.2.2/src
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/data/4res/ML0283/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/4res/ML0283/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 /data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -1119.97         -1125.34
2      -1119.82         -1125.49
--------------------------------------
TOTAL    -1119.89         -1125.42
--------------------------------------


Model parameter summaries over the runs sampled in files
"/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/4res/ML0283/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 "/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.861028    0.088522    0.290796    1.408786    0.829430   1501.00   1501.00    1.001
r(A<->C){all}   0.161649    0.020867    0.000032    0.458766    0.119957    143.33    192.71    1.003
r(A<->G){all}   0.230111    0.027794    0.000125    0.544075    0.199065    181.79    221.10    1.019
r(A<->T){all}   0.134121    0.014486    0.000315    0.380402    0.100733    249.46    309.45    1.000
r(C<->G){all}   0.154125    0.018934    0.000009    0.426339    0.115357    203.50    220.00    1.002
r(C<->T){all}   0.206309    0.023214    0.000149    0.507305    0.174665    156.74    187.90    1.000
r(G<->T){all}   0.113685    0.012391    0.000001    0.336751    0.078620    290.49    319.40    1.000
pi(A){all}      0.181391    0.000180    0.154571    0.206759    0.181140   1389.47   1428.90    1.000
pi(C){all}      0.302359    0.000263    0.273229    0.334548    0.302019   1134.84   1238.70    1.000
pi(G){all}      0.304822    0.000258    0.275305    0.336870    0.304705   1171.70   1325.12    1.000
pi(T){all}      0.211428    0.000200    0.185141    0.240102    0.211206   1246.94   1373.97    1.000
alpha{1,2}      0.244988    0.062526    0.027341    0.675257    0.171063   1327.81   1414.40    1.001
alpha{3}        0.353939    0.217451    0.000208    1.306860    0.173479   1182.29   1267.20    1.000
pinvar{all}     0.993301    0.000020    0.984550    0.999548    0.994380   1275.83   1358.55    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	-1082.911034
Model 2: PositiveSelection	-1078.17697
Model 0: one-ratio	-1081.848756
Model 7: beta	-1082.911006
Model 8: beta&w>1	-1080.169782


Model 0 vs 1	2.1245559999997568

Model 2 vs 1	9.468127999999979

Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: NC_011896_1_WP_012634412_1_293_MLBR_RS01430)

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

   153 P      1.000**       999.000
   174 A      1.000**       999.000

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: NC_011896_1_WP_012634412_1_293_MLBR_RS01430)

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

   153 P      0.870         7.292 +- 3.128
   174 A      0.975*        8.038 +- 2.332


Model 8 vs 7	5.482448000000204