--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Dec 04 14:42:27 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/351/Pkn-PK/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/351/Pkn-PK/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/351/Pkn-PK/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/351/Pkn-PK/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -15191.84 -15207.87
2 -15191.73 -15208.02
--------------------------------------
TOTAL -15191.79 -15207.95
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/351/Pkn-PK/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/351/Pkn-PK/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/351/Pkn-PK/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.082362 0.001600 1.005913 1.159620 1.082031 1387.92 1444.46 1.000
r(A<->C){all} 0.105026 0.000076 0.087275 0.121358 0.104553 885.20 947.52 1.000
r(A<->G){all} 0.284141 0.000199 0.258174 0.313312 0.283640 930.69 1036.46 1.000
r(A<->T){all} 0.110143 0.000116 0.090200 0.132337 0.110047 957.39 965.23 1.000
r(C<->G){all} 0.052019 0.000027 0.042276 0.062205 0.051882 866.76 1047.87 1.000
r(C<->T){all} 0.386952 0.000259 0.356076 0.419206 0.386530 825.50 866.39 1.000
r(G<->T){all} 0.061719 0.000043 0.049052 0.074385 0.061426 1123.89 1144.61 1.000
pi(A){all} 0.230954 0.000038 0.219017 0.242879 0.230781 836.31 855.31 1.001
pi(C){all} 0.274221 0.000040 0.261552 0.286440 0.274088 1028.27 1093.56 1.000
pi(G){all} 0.298420 0.000044 0.285912 0.311272 0.298501 1039.51 1043.45 1.001
pi(T){all} 0.196405 0.000030 0.185123 0.206419 0.196485 942.45 1043.83 1.000
alpha{1,2} 0.137292 0.000057 0.122655 0.152181 0.136985 1272.33 1386.66 1.000
alpha{3} 6.004522 1.366968 3.875579 8.301270 5.845014 1369.67 1392.28 1.000
pinvar{all} 0.339402 0.000426 0.298993 0.378911 0.340118 1081.95 1146.18 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 -13983.905481
Model 2: PositiveSelection -13983.905884
Model 0: one-ratio -14182.075663
Model 3: discrete -13970.417068
Model 7: beta -13975.883712
Model 8: beta&w>1 -13971.558664
Model 0 vs 1 396.3403639999997
Model 2 vs 1 8.060000000114087E-4
Model 8 vs 7 8.650096000001213
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Pkn-PK)
Pr(w>1) post mean +- SE for w
28 A 0.866 1.277
33 I 0.866 1.276
35 R 0.827 1.235
75 F 0.900 1.312
78 E 0.741 1.146
447 I 0.557 0.952
859 S 0.960* 1.375
860 A 0.966* 1.380
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_Pkn-PK)
Pr(w>1) post mean +- SE for w
28 A 0.929 1.440 +- 0.221
33 I 0.929 1.441 +- 0.221
34 A 0.607 1.103 +- 0.512
35 R 0.906 1.420 +- 0.253
47 R 0.537 1.026 +- 0.532
50 T 0.536 1.050 +- 0.503
72 S 0.546 1.036 +- 0.530
73 Y 0.525 1.010 +- 0.537
75 F 0.944 1.453 +- 0.196
76 D 0.536 1.048 +- 0.504
78 E 0.874 1.390 +- 0.296
230 N 0.522 1.036 +- 0.504
237 A 0.779 1.287 +- 0.413
418 Q 0.501 0.939 +- 0.589
447 I 0.823 1.329 +- 0.381
673 L 0.743 1.261 +- 0.418
676 S 0.595 1.109 +- 0.491
783 S 0.508 0.994 +- 0.537
809 T 0.606 1.103 +- 0.512
849 S 0.520 0.963 +- 0.585
859 S 0.970* 1.476 +- 0.139
860 A 0.968* 1.475 +- 0.142
1031 R 0.696 1.182 +- 0.499
