--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Tue Nov 07 03:26:49 WET 2017
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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/ADOPS1/Zikaomegamapresults/NS1/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zikaomegamapresults/NS1/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/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -4376.66 -4546.23
2 -4376.38 -4530.74
--------------------------------------
TOTAL -4376.51 -4545.53
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/Zikaomegamapresults/NS1/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/Zikaomegamapresults/NS1/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 2.098115 0.687712 1.336889 4.039509 1.756498 12.15 13.04 1.047
r(A<->C){all} 0.016865 0.000040 0.004876 0.028354 0.016897 20.56 31.92 1.036
r(A<->G){all} 0.111393 0.001376 0.034540 0.166740 0.119568 13.73 17.06 1.064
r(A<->T){all} 0.017820 0.000046 0.005320 0.030238 0.017690 20.24 32.57 1.034
r(C<->G){all} 0.008134 0.000016 0.001585 0.015943 0.007554 42.84 83.76 1.022
r(C<->T){all} 0.827348 0.002742 0.752118 0.937947 0.814481 13.40 16.30 1.066
r(G<->T){all} 0.018440 0.000043 0.005989 0.030749 0.018264 27.64 39.31 1.031
pi(A){all} 0.278333 0.000158 0.252525 0.301664 0.277975 234.30 410.08 1.000
pi(C){all} 0.222977 0.000124 0.201604 0.244600 0.222695 587.44 661.82 1.001
pi(G){all} 0.283955 0.000163 0.258674 0.308171 0.284026 671.65 672.44 1.000
pi(T){all} 0.214735 0.000122 0.192840 0.235669 0.214878 167.44 284.21 1.001
alpha{1,2} 0.121763 0.000223 0.091607 0.149307 0.122668 19.80 27.14 1.028
alpha{3} 2.304199 0.970799 0.515733 3.927971 2.342646 19.04 24.56 1.048
pinvar{all} 0.166874 0.001484 0.086596 0.238748 0.167303 541.37 787.88 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 -4230.377484
Model 2: PositiveSelection -4230.377484
Model 0: one-ratio -4250.007631
Model 3: discrete -4224.94038
Model 7: beta -4225.062473
Model 8: beta&w>1 -4225.062647
Model 0 vs 1 39.26029400000152
Model 2 vs 1 0.0
Model 8 vs 7 3.479999995761318E-4
