--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Thu Jan 23 17:03:42 GMT 2020
codeml.models=0 1 2 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=/usr/bin/
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb
tcoffee.bin=t_coffee
mrbayes.dir=/opt/mrbayes_3.2.2/src
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/data/4res/ML0283/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/4res/ML0283/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 /data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -1119.97 -1125.34
2 -1119.82 -1125.49
--------------------------------------
TOTAL -1119.89 -1125.42
--------------------------------------
Model parameter summaries over the runs sampled in files
"/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/data/4res/ML0283/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 "/data/4res/ML0283/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.861028 0.088522 0.290796 1.408786 0.829430 1501.00 1501.00 1.001
r(A<->C){all} 0.161649 0.020867 0.000032 0.458766 0.119957 143.33 192.71 1.003
r(A<->G){all} 0.230111 0.027794 0.000125 0.544075 0.199065 181.79 221.10 1.019
r(A<->T){all} 0.134121 0.014486 0.000315 0.380402 0.100733 249.46 309.45 1.000
r(C<->G){all} 0.154125 0.018934 0.000009 0.426339 0.115357 203.50 220.00 1.002
r(C<->T){all} 0.206309 0.023214 0.000149 0.507305 0.174665 156.74 187.90 1.000
r(G<->T){all} 0.113685 0.012391 0.000001 0.336751 0.078620 290.49 319.40 1.000
pi(A){all} 0.181391 0.000180 0.154571 0.206759 0.181140 1389.47 1428.90 1.000
pi(C){all} 0.302359 0.000263 0.273229 0.334548 0.302019 1134.84 1238.70 1.000
pi(G){all} 0.304822 0.000258 0.275305 0.336870 0.304705 1171.70 1325.12 1.000
pi(T){all} 0.211428 0.000200 0.185141 0.240102 0.211206 1246.94 1373.97 1.000
alpha{1,2} 0.244988 0.062526 0.027341 0.675257 0.171063 1327.81 1414.40 1.001
alpha{3} 0.353939 0.217451 0.000208 1.306860 0.173479 1182.29 1267.20 1.000
pinvar{all} 0.993301 0.000020 0.984550 0.999548 0.994380 1275.83 1358.55 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 -1082.911034
Model 2: PositiveSelection -1078.17697
Model 0: one-ratio -1081.848756
Model 7: beta -1082.911006
Model 8: beta&w>1 -1080.169782
Model 0 vs 1 2.1245559999997568
Model 2 vs 1 9.468127999999979
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: NC_011896_1_WP_012634412_1_293_MLBR_RS01430)
Pr(w>1) post mean +- SE for w
153 P 1.000** 999.000
174 A 1.000** 999.000
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: NC_011896_1_WP_012634412_1_293_MLBR_RS01430)
Pr(w>1) post mean +- SE for w
153 P 0.870 7.292 +- 3.128
174 A 0.975* 8.038 +- 2.332
Model 8 vs 7 5.482448000000204
