--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Nov 17 16:51:28 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/106/CG3036-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/106/CG3036-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/106/CG3036-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/106/CG3036-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -5673.16 -5690.53
2 -5673.63 -5688.30
--------------------------------------
TOTAL -5673.37 -5689.94
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/106/CG3036-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/106/CG3036-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/106/CG3036-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} 1.147074 0.006543 0.985517 1.295303 1.144048 1232.60 1366.80 1.000
r(A<->C){all} 0.108350 0.000274 0.077547 0.142156 0.107783 991.44 1041.45 1.001
r(A<->G){all} 0.200322 0.000507 0.157454 0.244977 0.199729 1073.41 1077.47 1.000
r(A<->T){all} 0.175721 0.000556 0.129862 0.220362 0.175040 626.37 718.30 1.001
r(C<->G){all} 0.061753 0.000093 0.043299 0.081344 0.061382 886.76 953.95 1.000
r(C<->T){all} 0.388730 0.000844 0.334164 0.443266 0.387940 771.23 853.83 1.001
r(G<->T){all} 0.065124 0.000147 0.041265 0.088163 0.064471 1216.62 1240.19 1.000
pi(A){all} 0.175387 0.000084 0.158463 0.194255 0.175219 1024.16 1141.11 1.000
pi(C){all} 0.307543 0.000123 0.286158 0.329346 0.307479 1026.55 1072.19 1.000
pi(G){all} 0.271962 0.000115 0.251601 0.292927 0.271682 1104.41 1151.47 1.000
pi(T){all} 0.245108 0.000098 0.226863 0.265377 0.244960 1089.73 1137.52 1.000
alpha{1,2} 0.179498 0.000355 0.144139 0.215582 0.178064 1181.81 1237.19 1.000
alpha{3} 3.440839 0.814150 1.838829 5.222487 3.320499 1266.62 1314.36 1.000
pinvar{all} 0.372117 0.001250 0.304319 0.440758 0.373297 1284.12 1289.65 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 -5172.501475
Model 2: PositiveSelection -5172.501497
Model 0: one-ratio -5253.724355
Model 3: discrete -5169.60076
Model 7: beta -5177.03905
Model 8: beta&w>1 -5169.6457
Model 0 vs 1 162.44576000000052
Model 2 vs 1 4.400000034365803E-5
Model 8 vs 7 14.786700000000565
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_CG3036-PA)
Pr(w>1) post mean +- SE for w
49 R 0.730 1.078
54 S 0.978* 1.374
55 V 0.589 0.909
59 L 0.898 1.280
60 V 0.992** 1.391
63 S 0.985* 1.383
66 A 0.993** 1.392
74 P 0.970* 1.365
77 S 0.951* 1.343
230 S 0.811 1.178
423 K 0.968* 1.363
425 Q 0.994** 1.393
444 A 0.726 1.074
482 E 0.810 1.177
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_CG3036-PA)
Pr(w>1) post mean +- SE for w
49 R 0.657 1.146 +- 0.550
54 S 0.909 1.441 +- 0.299
55 V 0.524 0.980 +- 0.597
59 L 0.810 1.336 +- 0.418
60 V 0.908 1.442 +- 0.285
63 S 0.896 1.430 +- 0.303
66 A 0.938 1.469 +- 0.252
74 P 0.835 1.371 +- 0.360
77 S 0.786 1.323 +- 0.399
230 S 0.688 1.205 +- 0.492
423 K 0.869 1.402 +- 0.339
425 Q 0.945 1.475 +- 0.243
444 A 0.663 1.151 +- 0.553
482 E 0.668 1.186 +- 0.493
