--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 17:58:59 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S5_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S5_17/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/ADOPS1/pet1/Phyb_S5_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13478.90 -13500.27
2 -13479.24 -13499.58
--------------------------------------
TOTAL -13479.06 -13499.98
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S5_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S5_17/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/ADOPS1/pet1/Phyb_S5_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.420668 0.011972 3.201478 3.625449 3.421105 1460.78 1480.89 1.000
r(A<->C){all} 0.137647 0.000102 0.117249 0.156196 0.137428 891.21 899.86 1.000
r(A<->G){all} 0.281939 0.000201 0.253416 0.308478 0.281750 567.36 660.11 1.003
r(A<->T){all} 0.094113 0.000045 0.081480 0.107741 0.093923 779.78 870.86 1.000
r(C<->G){all} 0.142588 0.000128 0.120515 0.163674 0.142611 792.17 921.67 1.000
r(C<->T){all} 0.263134 0.000178 0.237682 0.290508 0.262761 526.04 630.95 1.001
r(G<->T){all} 0.080579 0.000051 0.066698 0.094305 0.080431 834.67 913.55 1.002
pi(A){all} 0.307577 0.000092 0.288378 0.325334 0.307827 796.66 928.74 1.002
pi(C){all} 0.172195 0.000054 0.158925 0.187506 0.171982 840.60 894.32 1.000
pi(G){all} 0.193027 0.000060 0.177381 0.207096 0.192947 806.41 870.62 1.000
pi(T){all} 0.327202 0.000099 0.307719 0.346604 0.326991 769.40 849.36 1.001
alpha{1,2} 1.394142 0.033327 1.059722 1.757574 1.378958 992.78 1142.89 1.000
alpha{3} 4.998646 0.970768 3.258595 6.986072 4.908467 1224.89 1362.95 1.001
pinvar{all} 0.070981 0.000393 0.030510 0.110297 0.071150 1157.35 1205.17 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 -12069.555585
Model 2: PositiveSelection -12065.574693
Model 0: one-ratio -12265.094918
Model 3: discrete -12031.983346
Model 7: beta -12044.394849
Model 8: beta&w>1 -12027.651706
Model 0 vs 1 391.07866600000125
Model 2 vs 1 7.96178399999917
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Phybrida_S5_FBX2_AB932974)
Pr(w>1) post mean +- SE for w
53 A 0.537 1.647
69 Q 0.702 1.845
103 I 0.532 1.640
121 I 0.946 2.138
182 L 0.567 1.682
201 F 0.813 1.979
204 L 0.612 1.736
220 T 0.526 1.633
353 N 0.614 1.739
357 T 0.600 1.722
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: 1_Phybrida_S5_FBX2_AB932974)
Pr(w>1) post mean +- SE for w
53 A 0.554 1.735 +- 0.725
69 Q 0.711 1.957 +- 0.693
103 I 0.564 1.757 +- 0.730
121 I 0.937 2.267 +- 0.507
182 L 0.569 1.750 +- 0.721
201 F 0.828 2.131 +- 0.624
204 L 0.613 1.813 +- 0.717
220 T 0.535 1.705 +- 0.721
353 N 0.619 1.823 +- 0.718
357 T 0.614 1.821 +- 0.721
Model 8 vs 7 33.48628599999938
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: 1_Phybrida_S5_FBX2_AB932974)
Pr(w>1) post mean +- SE for w
50 P 0.662 1.264
53 A 0.934 1.495
67 P 0.769 1.357
69 Q 0.963* 1.519
100 T 0.851 1.429
103 I 0.924 1.488
120 N 0.912 1.477
121 I 0.992** 1.543
150 S 0.572 1.185
152 N 0.734 1.330
162 T 0.868 1.442
179 F 0.637 1.245
182 L 0.944 1.504
201 F 0.971* 1.526
204 L 0.954* 1.512
205 Y 0.850 1.425
220 T 0.933 1.495
221 V 0.881 1.452
247 C 0.637 1.252
266 G 0.614 1.228
268 E 0.531 1.152
271 E 0.875 1.447
340 K 0.826 1.408
353 N 0.953* 1.511
356 S 0.592 1.212
357 T 0.941 1.501
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: 1_Phybrida_S5_FBX2_AB932974)
Pr(w>1) post mean +- SE for w
53 A 0.825 1.389 +- 0.279
67 P 0.583 1.202 +- 0.376
69 Q 0.888 1.434 +- 0.234
100 T 0.682 1.285 +- 0.336
103 I 0.808 1.376 +- 0.291
120 N 0.786 1.359 +- 0.303
121 I 0.967* 1.488 +- 0.149
152 N 0.538 1.172 +- 0.370
162 T 0.712 1.305 +- 0.332
182 L 0.845 1.403 +- 0.264
201 F 0.909 1.448 +- 0.218
204 L 0.867 1.419 +- 0.249
205 Y 0.689 1.284 +- 0.348
220 T 0.823 1.387 +- 0.279
221 V 0.733 1.321 +- 0.329
271 E 0.721 1.312 +- 0.326
340 K 0.647 1.259 +- 0.344
353 N 0.866 1.418 +- 0.251
357 T 0.841 1.400 +- 0.270
