--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Nov 21 17:50:52 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/295/Lnk-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/295/Lnk-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/295/Lnk-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/295/Lnk-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -8840.35 -8856.15
2 -8840.28 -8857.57
--------------------------------------
TOTAL -8840.32 -8857.09
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/295/Lnk-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/295/Lnk-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/295/Lnk-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} 1.284705 0.004617 1.156776 1.421156 1.282137 1501.00 1501.00 1.000
r(A<->C){all} 0.106764 0.000122 0.084541 0.127284 0.106438 1104.97 1158.69 1.000
r(A<->G){all} 0.215512 0.000297 0.181407 0.247859 0.215202 784.46 916.38 1.000
r(A<->T){all} 0.124403 0.000221 0.096402 0.154537 0.123544 960.58 1026.03 1.000
r(C<->G){all} 0.074961 0.000067 0.059240 0.090318 0.074799 1057.26 1221.28 1.000
r(C<->T){all} 0.405653 0.000511 0.363822 0.452462 0.405706 619.16 831.55 1.000
r(G<->T){all} 0.072706 0.000106 0.053948 0.092929 0.072406 1069.72 1155.14 1.000
pi(A){all} 0.233749 0.000065 0.218423 0.249415 0.233731 916.11 1208.55 1.001
pi(C){all} 0.292704 0.000078 0.276392 0.311182 0.292598 1160.42 1177.72 1.000
pi(G){all} 0.296798 0.000082 0.280657 0.316429 0.296715 930.64 1004.97 1.000
pi(T){all} 0.176749 0.000050 0.162621 0.190314 0.176623 836.70 1056.13 1.000
alpha{1,2} 0.165202 0.000141 0.143230 0.188728 0.164777 1350.26 1406.98 1.003
alpha{3} 4.526188 0.881151 2.832990 6.324751 4.418485 1264.23 1380.02 1.000
pinvar{all} 0.367436 0.000634 0.318377 0.419257 0.367980 1038.18 1208.99 1.001
------------------------------------------------------------------------------------------------------
* 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 -7916.756018
Model 2: PositiveSelection -7916.756039
Model 0: one-ratio -7992.480109
Model 3: discrete -7907.483779
Model 7: beta -7913.023214
Model 8: beta&w>1 -7908.266947
Model 0 vs 1 151.4481820000001
Model 2 vs 1 4.199999966658652E-5
Model 8 vs 7 9.512533999999505
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_Lnk-PA)
Pr(w>1) post mean +- SE for w
36 A 0.731 1.131
323 S 0.940 1.372
531 S 0.608 0.986
543 N 0.932 1.362
571 S 0.563 0.934
576 T 0.700 1.094
681 G 0.991** 1.429
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_Lnk-PA)
Pr(w>1) post mean +- SE for w
36 A 0.804 1.325 +- 0.377
323 S 0.918 1.436 +- 0.245
531 S 0.770 1.282 +- 0.423
543 N 0.917 1.434 +- 0.249
571 S 0.741 1.252 +- 0.444
576 T 0.790 1.310 +- 0.390
681 G 0.972* 1.483 +- 0.150
