--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Nov 07 10:38:53 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/161/CG46244-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/161/CG46244-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/161/CG46244-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/161/CG46244-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -146.62 -158.03
2 -146.29 -159.66
--------------------------------------
TOTAL -146.44 -159.15
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/161/CG46244-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/161/CG46244-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/161/CG46244-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} 1.935610 0.198518 1.111090 2.837366 1.903942 1014.70 1156.25 1.000
r(A<->C){all} 0.108573 0.011164 0.000001 0.306852 0.078195 296.03 358.02 1.001
r(A<->G){all} 0.236642 0.027127 0.000356 0.546968 0.207967 209.51 223.41 1.000
r(A<->T){all} 0.042910 0.002608 0.000012 0.146012 0.025807 318.14 466.27 1.003
r(C<->G){all} 0.139977 0.017977 0.000027 0.408171 0.099930 155.84 158.35 1.002
r(C<->T){all} 0.300297 0.030618 0.029522 0.652046 0.272245 113.00 129.07 1.005
r(G<->T){all} 0.171602 0.018371 0.000343 0.438034 0.139495 266.37 294.52 1.006
pi(A){all} 0.303991 0.002556 0.204507 0.400660 0.303246 991.79 1131.80 1.000
pi(C){all} 0.173664 0.001569 0.094457 0.245215 0.170129 1091.75 1120.09 1.001
pi(G){all} 0.180034 0.001702 0.102256 0.258420 0.177207 1079.36 1244.71 1.001
pi(T){all} 0.342310 0.002720 0.243510 0.445177 0.340408 1168.26 1218.77 1.000
alpha{1,2} 0.314421 0.089594 0.004390 0.904983 0.212644 1255.95 1326.59 1.000
alpha{3} 0.357305 0.086089 0.049131 0.916327 0.270757 1394.33 1394.48 1.000
pinvar{all} 0.866638 0.004713 0.734314 0.970401 0.879896 1155.91 1199.63 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 -166.133028
Model 2: PositiveSelection -154.776127
Model 0: one-ratio -175.373989
Model 3: discrete -154.776127
Model 7: beta -166.137368
Model 8: beta&w>1 -154.776122
Model 0 vs 1 18.481921999999997
Model 2 vs 1 22.713801999999987
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_CG46244-PA)
Pr(w>1) post mean +- SE for w
9 H 1.000** 47.379
19 S 1.000** 47.379
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_CG46244-PA)
Pr(w>1) post mean +- SE for w
9 H 0.988* 9.485 +- 1.505
19 S 1.000** 9.588 +- 1.172
Model 8 vs 7 22.722492000000045
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_CG46244-PA)
Pr(w>1) post mean +- SE for w
9 H 1.000** 47.379
19 S 1.000** 47.379
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_CG46244-PA)
Pr(w>1) post mean +- SE for w
9 H 0.995** 9.545 +- 1.328
19 S 1.000** 9.589 +- 1.172
