--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Mon Apr 16 13:52:01 WEST 2018
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=
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AM/batch2/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/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -11370.18 -11414.43
2 -11370.19 -11414.59
--------------------------------------
TOTAL -11370.18 -11414.51
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/HIV1_AM/batch2/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/HIV1_AM/batch2/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 6.788471 0.094836 6.155887 7.368659 6.786524 676.34 821.55 1.000
r(A<->C){all} 0.107162 0.000070 0.091007 0.123545 0.106991 668.05 705.78 1.000
r(A<->G){all} 0.310907 0.000370 0.272288 0.347417 0.311561 319.83 408.85 1.000
r(A<->T){all} 0.093456 0.000072 0.077172 0.109695 0.093146 643.67 691.79 1.000
r(C<->G){all} 0.063819 0.000057 0.048840 0.078160 0.063342 729.08 757.80 1.000
r(C<->T){all} 0.329600 0.000420 0.291438 0.371954 0.328484 319.37 437.92 1.000
r(G<->T){all} 0.095055 0.000090 0.077447 0.114257 0.094688 723.23 753.85 1.003
pi(A){all} 0.353395 0.000149 0.330538 0.377653 0.353542 569.64 579.71 1.000
pi(C){all} 0.221142 0.000115 0.199015 0.241226 0.221232 588.32 613.62 1.001
pi(G){all} 0.241231 0.000118 0.220986 0.262965 0.241322 647.19 677.17 1.001
pi(T){all} 0.184232 0.000091 0.166427 0.203442 0.184077 588.54 626.01 1.000
alpha{1,2} 0.461161 0.001704 0.385411 0.542779 0.458314 1030.56 1175.59 1.000
alpha{3} 2.270255 0.118429 1.625646 2.950286 2.248987 1254.35 1307.79 1.000
pinvar{all} 0.068206 0.000523 0.025267 0.113319 0.066902 858.76 1048.13 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 -8780.802191
Model 2: PositiveSelection -8725.666742
Model 0: one-ratio -9263.633309
Model 3: discrete -8701.755116
Model 7: beta -8732.755948
Model 8: beta&w>1 -8686.864626
Model 0 vs 1 965.6622360000001
Model 2 vs 1 110.27089800000249
Additional information for M1 vs M2:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.ZA.08.as03_0513.KM262928_)
Pr(w>1) post mean +- SE for w
8 P 0.820 2.566
9 N 0.997** 2.904
107 V 1.000** 2.910
125 R 0.999** 2.908
131 C 0.997** 2.904
149 M 1.000** 2.910
155 S 1.000** 2.910
161 L 0.989* 2.889
165 K 1.000** 2.910
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: C.ZA.08.as03_0513.KM262928_)
Pr(w>1) post mean +- SE for w
8 P 0.789 2.363 +- 0.798
9 N 0.996** 2.784 +- 0.469
107 V 1.000** 2.792 +- 0.455
125 R 0.998** 2.788 +- 0.460
131 C 0.995** 2.782 +- 0.470
149 M 1.000** 2.791 +- 0.455
155 S 1.000** 2.792 +- 0.455
161 L 0.975* 2.735 +- 0.521
165 K 1.000** 2.792 +- 0.455
Model 8 vs 7 91.78264399999898
Additional information for M7 vs M8:
Naive Empirical Bayes (NEB) analysis
Positively selected sites (*: P>95%; **: P>99%)
(amino acids refer to 1st sequence: C.ZA.08.as03_0513.KM262928_)
Pr(w>1) post mean +- SE for w
8 P 0.849 2.147
9 N 0.995** 2.360
107 V 1.000** 2.367
125 R 0.998** 2.364
131 C 0.995** 2.360
149 M 1.000** 2.366
155 S 1.000** 2.367
161 L 0.981* 2.340
165 K 1.000** 2.367
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: C.ZA.08.as03_0513.KM262928_)
Pr(w>1) post mean +- SE for w
8 P 0.777 2.148 +- 0.658
9 N 0.993** 2.488 +- 0.134
107 V 1.000** 2.500 +- 0.011
125 R 0.996** 2.494 +- 0.098
131 C 0.992** 2.488 +- 0.138
149 M 0.999** 2.499 +- 0.042
155 S 1.000** 2.500 +- 0.016
161 L 0.963* 2.442 +- 0.296
165 K 1.000** 2.500 +- 0.006
