--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sun Dec 04 13:24:16 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-PJ/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/351/Pkn-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/351/Pkn-PJ/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-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -13706.53 -13727.55
2 -13706.63 -13723.84
--------------------------------------
TOTAL -13706.58 -13726.89
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/351/Pkn-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/351/Pkn-PJ/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-PJ/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.089793 0.001872 1.008223 1.176852 1.087599 913.91 1139.25 1.000
r(A<->C){all} 0.099565 0.000075 0.082523 0.116192 0.099390 1106.97 1138.66 1.000
r(A<->G){all} 0.290694 0.000231 0.261583 0.320295 0.290627 864.47 966.87 1.001
r(A<->T){all} 0.099692 0.000118 0.079973 0.122064 0.099406 838.60 1067.35 1.000
r(C<->G){all} 0.051259 0.000029 0.041068 0.061680 0.051099 837.43 994.80 1.000
r(C<->T){all} 0.398263 0.000309 0.365589 0.433990 0.398142 637.05 736.01 1.000
r(G<->T){all} 0.060528 0.000047 0.047901 0.074099 0.060308 1205.58 1210.87 1.000
pi(A){all} 0.228636 0.000040 0.217282 0.242258 0.228545 945.63 1097.06 1.000
pi(C){all} 0.277478 0.000045 0.265177 0.291265 0.277415 1051.06 1143.27 1.001
pi(G){all} 0.297188 0.000047 0.283312 0.310239 0.297111 1235.02 1237.68 1.001
pi(T){all} 0.196698 0.000032 0.185369 0.207700 0.196714 1016.86 1044.51 1.000
alpha{1,2} 0.122951 0.000043 0.111116 0.136622 0.122725 1155.53 1214.86 1.000
alpha{3} 6.480990 1.510029 4.406620 9.031236 6.346462 1142.30 1267.54 1.000
pinvar{all} 0.376979 0.000375 0.337741 0.413902 0.377390 1333.13 1417.07 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 -12679.576314
Model 2: PositiveSelection -12676.328543
Model 0: one-ratio -12805.798265
Model 3: discrete -12672.776531
Model 7: beta -12680.258515
Model 8: beta&w>1 -12669.264961
Model 0 vs 1 252.44390199999907
Model 2 vs 1 6.495542000000569
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: D_melanogaster_Pkn-PJ)
Pr(w>1) post mean +- SE for w
785 A 0.986* 5.176
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-PJ)
Pr(w>1) post mean +- SE for w
162 A 0.663 1.335 +- 0.250
372 I 0.643 1.319 +- 0.268
598 L 0.527 1.264 +- 0.259
784 S 0.695 1.352 +- 0.245
785 A 0.955* 1.483 +- 0.136
957 R 0.553 1.244 +- 0.343
Model 8 vs 7 21.987107999997534
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-PJ)
Pr(w>1) post mean +- SE for w
784 S 0.527 2.026
785 A 1.000** 3.543
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-PJ)
Pr(w>1) post mean +- SE for w
155 N 0.565 1.081 +- 0.496
162 A 0.893 1.407 +- 0.283
372 I 0.836 1.344 +- 0.369
598 L 0.745 1.264 +- 0.418
708 S 0.552 1.043 +- 0.529
734 T 0.622 1.120 +- 0.508
774 S 0.529 0.974 +- 0.585
784 S 0.918 1.430 +- 0.249
785 A 0.998** 1.500 +- 0.048
824 S 0.538 1.053 +- 0.502
957 R 0.713 1.204 +- 0.487
