--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 11 00:23:15 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/186/CG7766-PI/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/186/CG7766-PI/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/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -11539.43 -11554.18
2 -11539.66 -11555.75
--------------------------------------
TOTAL -11539.54 -11555.25
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/186/CG7766-PI/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/186/CG7766-PI/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 1.067379 0.002614 0.966162 1.163345 1.065976 1254.09 1275.43 1.000
r(A<->C){all} 0.068732 0.000079 0.051549 0.085469 0.068382 952.67 1002.10 1.000
r(A<->G){all} 0.264734 0.000346 0.228525 0.300109 0.264395 808.69 895.02 1.001
r(A<->T){all} 0.081366 0.000223 0.052348 0.109316 0.080950 892.00 918.53 1.000
r(C<->G){all} 0.083404 0.000053 0.070788 0.099021 0.083396 911.27 1056.27 1.000
r(C<->T){all} 0.447695 0.000474 0.406903 0.489943 0.447763 741.45 796.60 1.001
r(G<->T){all} 0.054068 0.000073 0.038209 0.071405 0.053799 1023.34 1189.11 1.000
pi(A){all} 0.204385 0.000041 0.191904 0.216717 0.204396 966.66 986.85 1.001
pi(C){all} 0.314901 0.000048 0.301670 0.327894 0.314933 1122.40 1172.96 1.000
pi(G){all} 0.297791 0.000051 0.283613 0.311697 0.297620 1174.71 1218.66 1.000
pi(T){all} 0.182923 0.000035 0.172221 0.195143 0.182778 987.58 1118.99 1.000
alpha{1,2} 0.090361 0.000032 0.079550 0.101712 0.090096 1122.64 1221.85 1.000
alpha{3} 5.252143 1.120007 3.450028 7.374641 5.146481 1501.00 1501.00 1.000
pinvar{all} 0.464053 0.000328 0.429534 0.499126 0.464710 1089.45 1130.10 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 -10459.356263
Model 2: PositiveSelection -10459.356296
Model 0: one-ratio -10499.099989
Model 3: discrete -10455.540937
Model 7: beta -10471.433477
Model 8: beta&w>1 -10458.925832
Model 0 vs 1 79.48745200000121
Model 2 vs 1 6.600000051548705E-5
Model 8 vs 7 25.015289999999368
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
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_CG7766-PI)
Pr(w>1) post mean +- SE for w
