--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Dec 11 18:50:07 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_S7_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S7_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_S7_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -12905.52 -12924.82
2 -12905.11 -12925.88
--------------------------------------
TOTAL -12905.29 -12925.48
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/pet1/Phyb_S7_17/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/pet1/Phyb_S7_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_S7_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} 3.265825 0.010945 3.060720 3.474241 3.265414 1131.84 1316.42 1.000
r(A<->C){all} 0.132530 0.000101 0.112495 0.151564 0.132369 940.63 977.04 1.000
r(A<->G){all} 0.281056 0.000215 0.253615 0.310926 0.280915 648.22 704.45 1.000
r(A<->T){all} 0.092113 0.000045 0.079208 0.105429 0.091953 782.52 865.58 1.000
r(C<->G){all} 0.132405 0.000142 0.107499 0.154393 0.132072 864.06 915.17 1.000
r(C<->T){all} 0.272875 0.000204 0.245572 0.300234 0.272632 510.47 588.85 1.000
r(G<->T){all} 0.089021 0.000053 0.075026 0.103275 0.088755 1063.52 1072.25 1.000
pi(A){all} 0.315042 0.000095 0.295826 0.333611 0.314910 813.48 992.23 1.000
pi(C){all} 0.170247 0.000053 0.156773 0.185549 0.170085 826.64 890.93 1.000
pi(G){all} 0.190637 0.000062 0.175602 0.206216 0.190515 666.66 779.83 1.000
pi(T){all} 0.324075 0.000097 0.304861 0.342008 0.324242 676.78 807.59 1.000
alpha{1,2} 1.207140 0.019957 0.936557 1.469855 1.196074 1114.91 1170.17 1.000
alpha{3} 4.667186 0.968614 2.958926 6.556642 4.548687 1183.10 1296.78 1.000
pinvar{all} 0.046080 0.000394 0.007189 0.083306 0.046066 1099.09 1144.42 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 -11189.151276
Model 2: PositiveSelection -11180.433629
Model 0: one-ratio -11368.248896
Model 3: discrete -11143.550911
Model 7: beta -11176.030513
Model 8: beta&w>1 -11145.643265
Model 0 vs 1 358.1952399999973
Model 2 vs 1 17.435294000002614
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_S7_FBX1_AB932986)
Pr(w>1) post mean +- SE for w
50 T 0.888 2.009
64 P 0.791 1.899
66 G 0.946 2.076
97 E 0.654 1.744
118 E 0.895 2.017
158 R 0.853 1.969
177 Q 0.606 1.689
196 T 0.512 1.582
199 W 0.605 1.687
215 D 0.578 1.657
216 M 0.947 2.076
239 G 0.872 1.991
240 Y 0.891 2.012
263 D 0.676 1.768
348 S 0.648 1.736
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_S7_FBX1_AB932986)
Pr(w>1) post mean +- SE for w
50 T 0.861 2.287 +- 0.539
64 P 0.739 2.104 +- 0.671
66 G 0.937 2.399 +- 0.400
97 E 0.526 1.780 +- 0.752
118 E 0.873 2.304 +- 0.522
158 R 0.816 2.219 +- 0.598
216 M 0.942 2.407 +- 0.387
239 G 0.856 2.279 +- 0.548
240 Y 0.866 2.293 +- 0.533
263 D 0.547 1.812 +- 0.749
348 S 0.505 1.748 +- 0.750
Model 8 vs 7 60.77449599999818
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_S7_FBX1_AB932986)
Pr(w>1) post mean +- SE for w
50 T 0.991** 1.737
64 P 0.975* 1.721
66 G 0.997** 1.743
97 E 0.966* 1.711
98 Y 0.527 1.230
100 V 0.856 1.594
117 F 0.905 1.646
118 E 0.992** 1.738
119 V 0.633 1.347
146 N 0.685 1.404
148 G 0.911 1.652
158 R 0.988* 1.734
171 M 0.879 1.618
174 D 0.536 1.247
175 W 0.718 1.442
177 Q 0.944 1.688
196 T 0.904 1.645
199 W 0.949 1.692
200 L 0.889 1.628
215 D 0.950* 1.695
216 M 0.997** 1.743
230 N 0.504 1.204
239 G 0.988* 1.733
240 Y 0.993** 1.739
242 G 0.900 1.640
261 F 0.929 1.672
262 S 0.515 1.216
263 D 0.963* 1.708
266 T 0.909 1.650
335 E 0.782 1.515
348 S 0.957* 1.702
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_S7_FBX1_AB932986)
Pr(w>1) post mean +- SE for w
50 T 0.956* 2.024 +- 0.546
64 P 0.904 1.962 +- 0.601
66 G 0.980* 2.050 +- 0.519
97 E 0.837 1.861 +- 0.647
100 V 0.532 1.416 +- 0.696
117 F 0.673 1.627 +- 0.717
118 E 0.958* 2.027 +- 0.544
148 G 0.647 1.580 +- 0.708
158 R 0.943 2.009 +- 0.560
171 M 0.570 1.465 +- 0.703
177 Q 0.771 1.766 +- 0.686
196 T 0.709 1.693 +- 0.716
199 W 0.763 1.750 +- 0.685
200 L 0.597 1.506 +- 0.710
215 D 0.775 1.773 +- 0.678
216 M 0.979* 2.050 +- 0.520
239 G 0.946 2.016 +- 0.558
240 Y 0.960* 2.028 +- 0.542
242 G 0.629 1.554 +- 0.714
261 F 0.654 1.581 +- 0.695
263 D 0.834 1.858 +- 0.651
266 T 0.616 1.529 +- 0.700
348 S 0.813 1.827 +- 0.665
