--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 12 05:23:26 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/2/Ac76E-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/2/Ac76E-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Ac76E-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/2/Ac76E-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -12095.72 -12109.17
2 -12096.07 -12109.57
--------------------------------------
TOTAL -12095.88 -12109.39
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/2/Ac76E-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Ac76E-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/2/Ac76E-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} 0.667738 0.001077 0.607688 0.734053 0.667299 1369.07 1404.27 1.000
r(A<->C){all} 0.132980 0.000145 0.110058 0.156550 0.132675 1000.98 1063.28 1.000
r(A<->G){all} 0.278409 0.000338 0.243570 0.315766 0.277989 553.28 765.12 1.000
r(A<->T){all} 0.083024 0.000146 0.060075 0.106815 0.082461 997.80 1007.61 1.000
r(C<->G){all} 0.079235 0.000066 0.063511 0.095126 0.078988 1169.02 1262.46 1.000
r(C<->T){all} 0.357377 0.000372 0.319549 0.393800 0.356899 890.64 919.92 1.000
r(G<->T){all} 0.068975 0.000086 0.052048 0.088704 0.068709 885.23 984.01 1.000
pi(A){all} 0.224299 0.000037 0.211279 0.235209 0.224301 1086.43 1092.80 1.002
pi(C){all} 0.295933 0.000048 0.282434 0.309019 0.295890 915.59 990.93 1.000
pi(G){all} 0.271215 0.000045 0.257340 0.283481 0.271144 975.33 985.67 1.000
pi(T){all} 0.208553 0.000034 0.197596 0.220294 0.208700 1037.76 1053.67 1.000
alpha{1,2} 0.158194 0.000183 0.130695 0.184697 0.157601 1374.41 1437.70 1.000
alpha{3} 4.372858 1.064250 2.643965 6.559605 4.249739 1315.13 1326.77 1.000
pinvar{all} 0.432648 0.000645 0.384763 0.484567 0.433419 1297.82 1378.67 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 -11237.599668
Model 2: PositiveSelection -11237.599676
Model 0: one-ratio -11438.14586
Model 3: discrete -11235.836021
Model 7: beta -11242.134885
Model 8: beta&w>1 -11238.121944
Model 0 vs 1 401.0923839999996
Model 2 vs 1 1.599999814061448E-5
Model 8 vs 7 8.025881999998091
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_Ac76E-PA)
Pr(w>1) post mean +- SE for w
29 T 0.860 1.898
517 I 0.870 1.913
520 T 0.959* 2.048
655 Q 0.643 1.566
923 K 0.732 1.702
931 E 0.980* 2.080
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_Ac76E-PA)
Pr(w>1) post mean +- SE for w
8 T 0.839 1.348 +- 0.358
16 N 0.820 1.330 +- 0.375
17 A 0.691 1.169 +- 0.514
19 A 0.574 1.027 +- 0.573
25 D 0.797 1.313 +- 0.380
29 T 0.963* 1.469 +- 0.159
202 T 0.584 1.040 +- 0.569
512 T 0.634 1.136 +- 0.497
515 T 0.753 1.264 +- 0.427
517 I 0.967* 1.474 +- 0.146
518 K 0.795 1.311 +- 0.382
520 T 0.984* 1.488 +- 0.096
541 P 0.581 1.037 +- 0.569
543 A 0.590 1.044 +- 0.570
544 I 0.522 1.010 +- 0.534
595 H 0.520 1.007 +- 0.535
602 N 0.863 1.377 +- 0.318
603 D 0.564 1.055 +- 0.526
605 E 0.899 1.413 +- 0.267
606 P 0.755 1.272 +- 0.412
655 Q 0.911 1.420 +- 0.264
672 G 0.664 1.136 +- 0.532
674 A 0.578 1.069 +- 0.524
923 K 0.946 1.455 +- 0.191
927 S 0.763 1.270 +- 0.426
928 T 0.710 1.221 +- 0.451
931 E 0.990* 1.493 +- 0.075
932 S 0.576 1.070 +- 0.522
934 F 0.519 0.970 +- 0.576
935 S 0.578 1.032 +- 0.572
938 V 0.825 1.334 +- 0.372
940 S 0.809 1.325 +- 0.371
947 L 0.555 1.020 +- 0.561
952 Y 0.859 1.368 +- 0.336
1005 M 0.753 1.270 +- 0.413
1008 D 0.890 1.403 +- 0.282
1009 A 0.757 1.264 +- 0.430
1012 T 0.792 1.300 +- 0.402
1013 H 0.547 0.996 +- 0.579
1266 T 0.662 1.162 +- 0.490
