--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Wed Dec 07 18:25:18 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-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/402/Spn-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PD/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-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -23131.26 -23151.11
2 -23131.35 -23147.53
--------------------------------------
TOTAL -23131.31 -23150.44
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/402/Spn-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/402/Spn-PD/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-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.185786 0.001592 1.111795 1.264950 1.184923 1451.84 1476.42 1.000
r(A<->C){all} 0.093680 0.000053 0.081264 0.109927 0.093578 1013.44 1063.79 1.000
r(A<->G){all} 0.232758 0.000134 0.211238 0.255549 0.232688 675.70 780.33 1.000
r(A<->T){all} 0.132533 0.000111 0.112894 0.153474 0.132485 746.21 841.19 1.001
r(C<->G){all} 0.071252 0.000026 0.061802 0.081338 0.071084 964.16 1034.11 1.000
r(C<->T){all} 0.400727 0.000201 0.373714 0.429046 0.400812 649.48 753.99 1.000
r(G<->T){all} 0.069049 0.000045 0.056181 0.081946 0.068837 1147.19 1189.92 1.000
pi(A){all} 0.227729 0.000023 0.218134 0.236857 0.227685 770.69 894.14 1.000
pi(C){all} 0.312521 0.000028 0.302352 0.322690 0.312433 840.09 939.19 1.000
pi(G){all} 0.301175 0.000027 0.291094 0.311041 0.301459 761.40 930.83 1.000
pi(T){all} 0.158575 0.000015 0.151241 0.166236 0.158547 929.85 1021.36 1.000
alpha{1,2} 0.126793 0.000030 0.116724 0.137941 0.126596 1174.96 1241.92 1.001
alpha{3} 5.347355 0.967240 3.552709 7.221855 5.229253 1173.91 1308.49 1.000
pinvar{all} 0.370139 0.000253 0.338655 0.401719 0.370462 1276.06 1327.66 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 -20230.015021
Model 2: PositiveSelection -20230.015021
Model 0: one-ratio -20634.81645
Model 3: discrete -20202.114781
Model 7: beta -20207.938984
Model 8: beta&w>1 -20203.0268
Model 0 vs 1 809.6028579999984
Model 2 vs 1 0.0
Model 8 vs 7 9.824368000001414
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
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-PD)
Pr(w>1) post mean +- SE for w
143 I 0.766 1.282 +- 0.406
149 V 0.586 1.081 +- 0.519
167 Q 0.928 1.438 +- 0.226
184 L 0.813 1.333 +- 0.357
189 P 0.867 1.380 +- 0.313
190 S 0.576 1.065 +- 0.527
191 P 0.866 1.379 +- 0.315
196 S 0.727 1.243 +- 0.432
318 R 0.921 1.432 +- 0.239
319 L 0.537 1.028 +- 0.530
357 S 0.798 1.313 +- 0.383
378 T 0.826 1.346 +- 0.344
417 P 0.634 1.150 +- 0.475
490 S 0.706 1.210 +- 0.465
493 S 0.832 1.347 +- 0.350
497 S 0.738 1.260 +- 0.414
509 A 0.715 1.241 +- 0.422
553 A 0.892 1.408 +- 0.269
566 Q 0.582 1.101 +- 0.488
567 T 0.829 1.345 +- 0.351
643 S 0.742 1.246 +- 0.444
645 S 0.625 1.142 +- 0.479
647 L 0.519 1.027 +- 0.511
701 L 0.583 1.075 +- 0.523
809 S 0.593 1.086 +- 0.519
810 I 0.974* 1.480 +- 0.127
811 Q 0.853 1.368 +- 0.326
814 T 0.837 1.352 +- 0.345
922 F 0.845 1.363 +- 0.327
935 A 0.514 1.021 +- 0.512
1015 S 0.559 1.048 +- 0.529
1016 S 0.908 1.422 +- 0.252
1018 A 0.754 1.261 +- 0.433
1019 P 0.741 1.246 +- 0.443
1627 S 0.623 1.126 +- 0.499
1632 V 0.563 1.077 +- 0.498
1675 G 0.782 1.299 +- 0.392
1709 T 0.552 1.043 +- 0.528
1807 T 0.551 1.059 +- 0.507
1844 S 0.925 1.438 +- 0.222
