--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Dec 07 19:27:24 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/402/Spn-PE/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PE/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/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -19698.90 -19713.21
2 -19699.20 -19713.95
--------------------------------------
TOTAL -19699.04 -19713.65
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PE/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/402/Spn-PE/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.213465 0.001853 1.119721 1.288991 1.212543 1176.47 1218.16 1.000
r(A<->C){all} 0.096282 0.000059 0.081688 0.111408 0.096129 1118.36 1159.12 1.000
r(A<->G){all} 0.230257 0.000147 0.206437 0.253833 0.229974 1186.02 1187.98 1.000
r(A<->T){all} 0.137875 0.000126 0.115429 0.159439 0.137671 805.78 958.82 1.000
r(C<->G){all} 0.068004 0.000029 0.057887 0.078624 0.067981 1096.02 1101.69 1.000
r(C<->T){all} 0.397718 0.000232 0.368205 0.426746 0.397818 825.57 882.29 1.000
r(G<->T){all} 0.069864 0.000049 0.055925 0.082947 0.069802 861.36 1007.17 1.000
pi(A){all} 0.229079 0.000026 0.219368 0.239299 0.229031 1025.66 1050.86 1.000
pi(C){all} 0.305642 0.000031 0.294153 0.316267 0.305671 867.74 1031.60 1.000
pi(G){all} 0.305593 0.000033 0.293962 0.316209 0.305463 884.85 894.37 1.000
pi(T){all} 0.159686 0.000019 0.151348 0.168115 0.159607 881.00 995.50 1.000
alpha{1,2} 0.123166 0.000032 0.113050 0.135277 0.122967 1277.04 1321.00 1.000
alpha{3} 5.037804 0.792318 3.337747 6.672153 4.927351 1400.37 1413.03 1.002
pinvar{all} 0.363499 0.000293 0.330753 0.397261 0.363717 1176.05 1240.49 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 -17152.93027
Model 2: PositiveSelection -17152.930423
Model 0: one-ratio -17465.49826
Model 3: discrete -17125.27371
Model 7: beta -17137.087421
Model 8: beta&w>1 -17125.369446
Model 0 vs 1 625.1359799999991
Model 2 vs 1 3.060000017285347E-4
Model 8 vs 7 23.43594999999914
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_Spn-PE)
Pr(w>1) post mean +- SE for w
56 V 0.710 0.855
143 I 0.891 1.013
149 P 0.993** 1.102
166 Q 0.976* 1.087
183 L 0.852 0.979
188 P 0.939 1.055
189 S 0.729 0.872
195 S 0.874 0.998
273 P 0.535 0.703
317 R 0.901 1.022
318 L 0.652 0.805
356 S 0.927 1.044
377 T 0.948 1.062
410 S 0.622 0.779
415 P 0.829 0.959
488 S 0.803 0.936
491 S 0.938 1.054
495 S 0.914 1.033
507 A 0.930 1.047
551 A 0.983* 1.093
564 Q 0.876 1.000
565 T 0.943 1.058
641 S 0.811 0.943
643 S 0.806 0.939
645 L 0.728 0.871
699 L 0.675 0.825
720 V 0.649 0.802
805 T 0.641 0.795
808 S 0.701 0.848
809 I 0.999** 1.107
810 Q 0.998** 1.106
956 T 0.593 0.753
1013 S 0.597 0.757
1014 S 0.996** 1.104
1016 A 0.819 0.950
1017 P 0.822 0.953
1030 H 0.594 0.755
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_Spn-PE)
Pr(w>1) post mean +- SE for w
56 V 0.500 1.006 +- 0.514
143 I 0.769 1.285 +- 0.403
149 P 0.965* 1.472 +- 0.152
166 Q 0.923 1.434 +- 0.234
183 L 0.718 1.228 +- 0.448
188 P 0.857 1.371 +- 0.323
189 S 0.626 1.122 +- 0.508
195 S 0.740 1.256 +- 0.424
317 R 0.839 1.349 +- 0.355
318 L 0.523 1.010 +- 0.535
356 S 0.835 1.350 +- 0.347
377 T 0.807 1.328 +- 0.360
415 P 0.641 1.158 +- 0.472
488 S 0.710 1.215 +- 0.462
491 S 0.835 1.352 +- 0.343
495 S 0.751 1.273 +- 0.406
507 A 0.752 1.276 +- 0.400
551 A 0.887 1.404 +- 0.274
564 Q 0.656 1.181 +- 0.456
565 T 0.855 1.370 +- 0.324
641 S 0.734 1.238 +- 0.449
643 S 0.613 1.128 +- 0.484
645 L 0.520 1.028 +- 0.510
699 L 0.559 1.047 +- 0.530
805 T 0.501 0.985 +- 0.540
808 S 0.580 1.073 +- 0.522
809 I 0.989* 1.491 +- 0.082
810 Q 0.974* 1.480 +- 0.125
1014 S 0.965* 1.472 +- 0.150
1016 A 0.735 1.241 +- 0.446
1017 P 0.741 1.247 +- 0.443
