--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Oct 31 19:39:26 WET 2017
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=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Srevisao/S25_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S25_16Malus/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/Srevisao/S25_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -7352.52 -7368.80
2 -7352.63 -7369.41
--------------------------------------
TOTAL -7352.57 -7369.15
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Srevisao/S25_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Srevisao/S25_16Malus/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/Srevisao/S25_16Malus/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.457809 0.003645 1.336056 1.573508 1.456345 1301.71 1379.25 1.000
r(A<->C){all} 0.118840 0.000147 0.094239 0.141521 0.118425 859.91 978.17 1.000
r(A<->G){all} 0.296597 0.000333 0.262339 0.333668 0.296637 625.05 626.98 1.000
r(A<->T){all} 0.078653 0.000062 0.063631 0.094143 0.078476 1052.01 1107.37 1.001
r(C<->G){all} 0.160694 0.000257 0.129745 0.192216 0.160162 927.15 935.23 1.001
r(C<->T){all} 0.253888 0.000298 0.218780 0.285554 0.253665 663.22 741.84 1.000
r(G<->T){all} 0.091328 0.000094 0.073371 0.110552 0.090952 1015.18 1078.91 1.000
pi(A){all} 0.301323 0.000122 0.279741 0.322571 0.301124 895.70 993.34 1.001
pi(C){all} 0.172120 0.000075 0.155323 0.188541 0.172025 998.35 1019.17 1.000
pi(G){all} 0.189606 0.000085 0.171004 0.207233 0.189603 922.96 960.89 1.000
pi(T){all} 0.336951 0.000133 0.315352 0.360317 0.337070 902.06 988.80 1.001
alpha{1,2} 0.773094 0.013186 0.572259 0.990089 0.756407 1289.92 1324.73 1.000
alpha{3} 1.608514 0.146529 0.973086 2.357180 1.548033 1225.01 1243.84 1.000
pinvar{all} 0.041895 0.001133 0.000002 0.106346 0.034077 976.28 997.27 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 -1216.762323
Model 2: PositiveSelection -1210.792323
Model 0: one-ratio -1238.943124
Model 3: discrete -1210.631394
Model 7: beta -1218.019057
Model 8: beta&w>1 -1210.651417
Model 0 vs 1 44.36160199999995
Model 2 vs 1 11.940000000000055
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.867 2.709
19 Q 0.981* 2.932
20 Y 0.521 2.025
22 Y 0.934 2.840
26 A 0.791 2.559
36 T 0.899 2.771
37 T 0.702 2.382
51 E 0.989* 2.949
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: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.868 2.790 +- 1.034
19 Q 0.979* 3.041 +- 0.878
20 Y 0.540 1.994 +- 1.043
22 Y 0.918 2.868 +- 0.928
26 A 0.775 2.520 +- 1.034
36 T 0.888 2.809 +- 0.977
37 T 0.670 2.234 +- 1.001
51 E 0.987* 3.049 +- 0.854
66 I 0.504 1.876 +- 0.957
Model 8 vs 7 14.735279999999875
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.913 2.493
19 Q 0.987* 2.621
20 Y 0.653 2.032
22 Y 0.964* 2.582
26 A 0.879 2.434
36 T 0.940 2.539
37 T 0.839 2.366
51 E 0.994** 2.632
66 I 0.672 2.075
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: S25_SFBB1)
Pr(w>1) post mean +- SE for w
7 Q 0.941 2.495 +- 0.662
19 Q 0.992** 2.589 +- 0.559
20 Y 0.738 2.082 +- 0.866
22 Y 0.976* 2.556 +- 0.583
26 A 0.917 2.436 +- 0.680
29 H 0.550 1.710 +- 0.927
36 T 0.959* 2.526 +- 0.620
37 T 0.883 2.354 +- 0.701
51 E 0.996** 2.596 +- 0.548
53 Y 0.529 1.669 +- 0.857
66 I 0.762 2.113 +- 0.806
