--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Nov 05 02:01:55 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=/opt/ADOPS1/Ebolaaminoresults/vp24/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp24/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/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -3891.89 -3922.79
2 -3891.51 -3919.53
--------------------------------------
TOTAL -3891.68 -3922.13
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Ebolaaminoresults/vp24/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/Ebolaaminoresults/vp24/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 4.054835 0.105412 3.454792 4.714971 4.038131 961.18 1019.30 1.000
r(A<->C){all} 0.133750 0.000377 0.096895 0.171654 0.133364 841.57 888.40 1.000
r(A<->G){all} 0.304961 0.000907 0.243142 0.361515 0.304498 789.35 845.13 1.000
r(A<->T){all} 0.046135 0.000168 0.022236 0.071692 0.045258 1044.70 1047.72 1.000
r(C<->G){all} 0.017873 0.000108 0.000463 0.037294 0.016303 750.80 906.75 1.000
r(C<->T){all} 0.440652 0.001157 0.377534 0.507445 0.440138 741.63 785.49 1.000
r(G<->T){all} 0.056629 0.000194 0.031199 0.084487 0.055954 1067.58 1099.13 1.000
pi(A){all} 0.291027 0.000160 0.265597 0.314791 0.290737 1064.26 1089.46 1.000
pi(C){all} 0.230445 0.000118 0.209504 0.252417 0.230240 857.74 1009.58 1.000
pi(G){all} 0.207558 0.000128 0.185192 0.228653 0.207540 666.61 915.96 1.000
pi(T){all} 0.270970 0.000149 0.245140 0.293228 0.270866 1006.38 1116.96 1.000
alpha{1,2} 0.165518 0.000209 0.139985 0.196007 0.164526 1144.95 1268.60 1.000
alpha{3} 4.252383 1.069604 2.389553 6.254538 4.120725 1329.98 1404.12 1.000
pinvar{all} 0.037214 0.000535 0.000036 0.079521 0.034796 1314.97 1407.98 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 -3566.059905
Model 2: PositiveSelection -3566.059905
Model 0: one-ratio -3589.271015
Model 3: discrete -3544.960047
Model 7: beta -3547.782422
Model 8: beta&w>1 -3545.823393
Model 0 vs 1 46.42221999999947
Model 2 vs 1 0.0
Model 8 vs 7 3.918058000000201
