--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Nov 08 15:32:07 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/166/CG5151-PF/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/166/CG5151-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/166/CG5151-PF/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/166/CG5151-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -5083.72 -5101.85
2 -5083.89 -5100.74
--------------------------------------
TOTAL -5083.80 -5101.44
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/166/CG5151-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/166/CG5151-PF/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/166/CG5151-PF/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.700905 0.003266 0.592763 0.814960 0.698298 1304.33 1378.96 1.001
r(A<->C){all} 0.109343 0.000234 0.081469 0.140482 0.108634 888.73 960.89 1.000
r(A<->G){all} 0.199707 0.000518 0.157103 0.242215 0.198365 822.30 842.53 1.000
r(A<->T){all} 0.185639 0.000759 0.132655 0.239914 0.184025 909.44 1017.11 1.000
r(C<->G){all} 0.069245 0.000120 0.048455 0.091015 0.068522 1063.03 1105.51 1.000
r(C<->T){all} 0.338576 0.000866 0.282127 0.396102 0.338658 888.95 903.59 1.000
r(G<->T){all} 0.097491 0.000338 0.063437 0.135248 0.097010 906.58 913.13 1.000
pi(A){all} 0.239218 0.000108 0.218402 0.259765 0.239106 990.96 1046.71 1.000
pi(C){all} 0.340855 0.000133 0.319028 0.364161 0.340630 1087.34 1136.70 1.000
pi(G){all} 0.269703 0.000113 0.248525 0.290610 0.269454 1231.72 1244.42 1.000
pi(T){all} 0.150224 0.000080 0.132796 0.167270 0.150121 1043.80 1146.65 1.001
alpha{1,2} 0.265225 0.001765 0.194572 0.346574 0.259737 1314.95 1340.41 1.000
alpha{3} 3.010950 0.810517 1.438061 4.819418 2.926399 1418.81 1442.14 1.001
pinvar{all} 0.452561 0.001691 0.372007 0.530376 0.456120 1202.79 1351.89 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 -4163.924639
Model 2: PositiveSelection -4162.884275
Model 0: one-ratio -4217.146326
Model 3: discrete -4160.953607
Model 7: beta -4164.502343
Model 8: beta&w>1 -4161.139049
Model 0 vs 1 106.4433740000004
Model 2 vs 1 2.0807279999989987
Model 8 vs 7 6.726587999999538
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_CG5151-PF)
Pr(w>1) post mean +- SE for w
97 A 0.952* 3.365
293 T 0.967* 3.407
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_CG5151-PF)
Pr(w>1) post mean +- SE for w
97 A 0.969* 1.502 +- 0.219
98 A 0.858 1.396 +- 0.371
102 D 0.614 1.135 +- 0.513
252 A 0.680 1.207 +- 0.492
293 T 0.973* 1.505 +- 0.213
392 S 0.637 1.173 +- 0.477
394 S 0.861 1.403 +- 0.353
397 L 0.686 1.191 +- 0.537
398 A 0.904 1.444 +- 0.305
401 E 0.642 1.165 +- 0.504
403 T 0.752 1.293 +- 0.431
405 T 0.842 1.379 +- 0.386
