--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 12:36:20 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/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet/Paxi_S19_20/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/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -14047.73 -14074.62
2 -14047.44 -14069.20
--------------------------------------
TOTAL -14047.58 -14073.94
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet/Paxi_S19_20/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/pet/Paxi_S19_20/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 3.598672 0.012868 3.368540 3.809873 3.596539 1053.88 1106.94 1.000
r(A<->C){all} 0.139015 0.000096 0.119115 0.157120 0.138698 536.25 747.04 1.000
r(A<->G){all} 0.290778 0.000202 0.263196 0.317902 0.290555 618.79 659.38 1.000
r(A<->T){all} 0.096929 0.000042 0.084577 0.109928 0.096644 663.91 841.25 1.000
r(C<->G){all} 0.128216 0.000119 0.106659 0.148599 0.128136 528.78 592.09 1.000
r(C<->T){all} 0.266421 0.000168 0.240283 0.290463 0.265949 649.73 664.99 1.001
r(G<->T){all} 0.078641 0.000045 0.063917 0.090635 0.078496 920.81 936.48 1.000
pi(A){all} 0.307996 0.000087 0.289404 0.325417 0.308023 862.37 865.16 1.000
pi(C){all} 0.170940 0.000053 0.156548 0.185019 0.170769 801.50 850.29 1.000
pi(G){all} 0.190601 0.000061 0.175721 0.206406 0.190478 798.49 810.74 1.001
pi(T){all} 0.330462 0.000095 0.311838 0.349714 0.330531 740.28 804.73 1.000
alpha{1,2} 1.219535 0.021686 0.944315 1.502689 1.201737 1206.88 1222.70 1.000
alpha{3} 4.153370 0.614768 2.807966 5.784710 4.079843 1327.83 1376.67 1.000
pinvar{all} 0.033503 0.000354 0.000498 0.067122 0.031850 1186.02 1234.78 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 -11413.08794
Model 2: PositiveSelection -11410.099548
Model 0: one-ratio -11596.942392
Model 3: discrete -11371.713279
Model 7: beta -11389.075708
Model 8: beta&w>1 -11372.060231
Model 0 vs 1 367.7089040000028
Model 2 vs 1 5.976783999998588
Model 8 vs 7 34.03095400000166
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_Paxillaris_S19_FBX1_AB933053)
Pr(w>1) post mean +- SE for w
15 A 0.594 1.118
25 T 0.742 1.244
28 F 0.974* 1.428
42 Y 0.966* 1.421
44 F 0.984* 1.435
74 S 0.536 1.081
75 A 0.644 1.169
77 V 0.815 1.305
94 S 0.985* 1.435
95 L 0.982* 1.434
96 T 0.669 1.185
124 S 0.554 1.088
136 A 0.713 1.221
149 K 0.948 1.407
152 D 0.727 1.232
155 M 0.928 1.392
174 F 0.990** 1.440
177 W 0.930 1.393
178 L 0.658 1.176
193 D 0.894 1.365
194 V 0.941 1.402
207 N 0.791 1.283
238 M 0.747 1.250
240 S 0.601 1.129
243 T 0.801 1.293
312 E 0.727 1.235
325 A 0.972* 1.426
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_Paxillaris_S19_FBX1_AB933053)
Pr(w>1) post mean +- SE for w
28 F 0.886 1.435 +- 0.247
42 Y 0.868 1.422 +- 0.265
44 F 0.924 1.461 +- 0.215
77 V 0.529 1.167 +- 0.376
94 S 0.922 1.461 +- 0.215
95 L 0.915 1.456 +- 0.222
149 K 0.797 1.369 +- 0.300
155 M 0.756 1.337 +- 0.325
174 F 0.947 1.478 +- 0.189
177 W 0.756 1.338 +- 0.322
193 D 0.688 1.286 +- 0.355
194 V 0.791 1.365 +- 0.310
207 N 0.517 1.147 +- 0.385
243 T 0.511 1.148 +- 0.377
325 A 0.878 1.429 +- 0.253
