--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Thu Jan 23 14:58:34 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/11res/rplX/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/data/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/11res/rplX/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/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1       -431.04          -434.12
2       -431.05          -434.74
--------------------------------------
TOTAL     -431.05          -434.48
--------------------------------------


Model parameter summaries over the runs sampled in files
"/data/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/11res/rplX/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/11res/rplX/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         0.896429    0.090892    0.357445    1.494586    0.860553   1311.15   1406.07    1.000
r(A<->C){all}   0.167134    0.019857    0.000001    0.452945    0.128984    108.55    150.92    1.000
r(A<->G){all}   0.166594    0.019803    0.000026    0.457625    0.127979    160.09    204.21    1.001
r(A<->T){all}   0.165910    0.020053    0.000134    0.458103    0.128648    135.20    160.49    1.001
r(C<->G){all}   0.164438    0.020192    0.000075    0.458443    0.125735    186.93    200.46    1.000
r(C<->T){all}   0.165173    0.018522    0.000008    0.427901    0.129134    195.63    206.64    1.002
r(G<->T){all}   0.170750    0.019709    0.000027    0.445923    0.136580    244.13    269.52    1.006
pi(A){all}      0.263564    0.000630    0.214421    0.312594    0.262972   1276.50   1290.98    1.000
pi(C){all}      0.263014    0.000591    0.216419    0.310420    0.263317   1218.98   1309.75    1.000
pi(G){all}      0.307586    0.000629    0.260520    0.357932    0.307057   1161.78   1246.99    1.000
pi(T){all}      0.165836    0.000440    0.125786    0.206985    0.164949   1149.02   1176.22    1.000
alpha{1,2}      0.411714    0.218664    0.000197    1.341564    0.243621   1164.66   1269.92    1.000
alpha{3}        0.448791    0.229546    0.000306    1.401306    0.290476   1175.96   1318.68    1.001
pinvar{all}     0.994907    0.000038    0.983191    0.999998    0.996870   1328.33   1350.36    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	-406.399605
Model 2: PositiveSelection	-406.39957
Model 0: one-ratio	-406.399599
Model 7: beta	-406.399695
Model 8: beta&w>1	-406.39957


Model 0 vs 1	1.1999999969702912E-5

Model 2 vs 1	7.000000005064066E-5

Model 8 vs 7	2.500000000509317E-4