--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Dec 02 21:43:58 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/96/CG18304-PC/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/96/CG18304-PC/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/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -22674.84 -22691.88
2 -22675.05 -22692.12
--------------------------------------
TOTAL -22674.94 -22692.01
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/96/CG18304-PC/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/96/CG18304-PC/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.378362 0.001783 1.290439 1.457044 1.376656 1235.10 1368.05 1.000
r(A<->C){all} 0.087775 0.000038 0.075997 0.099652 0.087709 663.76 686.03 1.000
r(A<->G){all} 0.246503 0.000116 0.225354 0.267568 0.246621 798.18 855.01 1.000
r(A<->T){all} 0.144655 0.000113 0.125112 0.167140 0.144525 827.04 860.73 1.000
r(C<->G){all} 0.053813 0.000017 0.046109 0.062053 0.053715 1091.83 1139.29 1.000
r(C<->T){all} 0.392110 0.000191 0.366214 0.418865 0.392153 763.73 781.07 1.000
r(G<->T){all} 0.075145 0.000045 0.063069 0.088790 0.074932 875.30 958.96 1.000
pi(A){all} 0.273351 0.000032 0.263216 0.285246 0.273392 768.25 896.44 1.000
pi(C){all} 0.270967 0.000029 0.260474 0.281282 0.270728 866.50 969.68 1.000
pi(G){all} 0.297671 0.000032 0.287441 0.309208 0.297606 909.31 960.24 1.000
pi(T){all} 0.158011 0.000019 0.149258 0.166010 0.157955 560.60 719.01 1.000
alpha{1,2} 0.153716 0.000044 0.141233 0.166938 0.153573 1212.70 1325.04 1.000
alpha{3} 5.058830 0.710990 3.582431 6.711710 4.970144 1285.73 1339.59 1.000
pinvar{all} 0.305418 0.000279 0.273403 0.339705 0.305716 1323.45 1346.14 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 -20645.365115
Model 2: PositiveSelection -20645.365115
Model 0: one-ratio -20914.180362
Model 3: discrete -20570.698627
Model 7: beta -20577.320931
Model 8: beta&w>1 -20570.437721
Model 0 vs 1 537.6304939999973
Model 2 vs 1 0.0
Model 8 vs 7 13.766419999999925
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_CG18304-PC)
Pr(w>1) post mean +- SE for w
117 S 0.584 0.806
287 S 0.573 0.796
289 A 0.980* 1.145
290 S 0.943 1.113
303 I 0.930 1.102
306 T 0.961* 1.129
307 A 0.879 1.058
309 A 0.648 0.860
312 S 0.888 1.066
890 S 0.749 0.947
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_CG18304-PC)
Pr(w>1) post mean +- SE for w
78 A 0.650 1.151 +- 0.493
117 S 0.743 1.261 +- 0.418
149 I 0.731 1.237 +- 0.447
214 P 0.586 1.081 +- 0.518
215 T 0.533 1.023 +- 0.532
234 L 0.672 1.189 +- 0.459
274 V 0.555 1.068 +- 0.500
287 S 0.733 1.251 +- 0.425
289 A 0.973* 1.479 +- 0.129
290 S 0.923 1.437 +- 0.223
301 A 0.507 0.994 +- 0.536
303 I 0.947 1.456 +- 0.190
306 T 0.935 1.448 +- 0.203
307 A 0.874 1.394 +- 0.287
309 A 0.795 1.311 +- 0.381
312 S 0.924 1.435 +- 0.231
591 L 0.560 1.076 +- 0.497
849 G 0.650 1.157 +- 0.484
890 S 0.818 1.338 +- 0.351
908 A 0.522 1.031 +- 0.509
1020 A 0.553 1.068 +- 0.498
