--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Jul 11 03:09:26 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=/opt/ADOPS1/DNG_N3/NS4A_3/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_3/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/DNG_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3649.06         -3698.58
2      -3649.37         -3696.21
--------------------------------------
TOTAL    -3649.20         -3697.98
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_3/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/DNG_N3/NS4A_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         8.635339    0.433553    7.462612   10.081880    8.625848    918.75    950.66    1.000
r(A<->C){all}   0.029162    0.000076    0.012416    0.045706    0.028648    710.10    772.91    1.000
r(A<->G){all}   0.223048    0.000623    0.175226    0.272317    0.222653    460.76    572.48    1.000
r(A<->T){all}   0.070170    0.000159    0.048357    0.097240    0.069425    694.35    806.58    1.000
r(C<->G){all}   0.015883    0.000069    0.000799    0.031497    0.014855    562.43    722.35    1.001
r(C<->T){all}   0.619607    0.000918    0.554356    0.674514    0.620210    566.99    631.40    1.001
r(G<->T){all}   0.042131    0.000146    0.019135    0.064986    0.041420    774.37    829.94    1.003
pi(A){all}      0.309824    0.000259    0.276517    0.339625    0.309986    841.92    864.57    1.001
pi(C){all}      0.247676    0.000222    0.217510    0.275068    0.247809    772.97    798.19    1.001
pi(G){all}      0.236724    0.000210    0.209267    0.265741    0.236594    649.58    702.87    1.000
pi(T){all}      0.205775    0.000167    0.181126    0.231578    0.205291    776.31    833.94    1.000
alpha{1,2}      0.231096    0.000473    0.187919    0.273066    0.229925   1340.49   1420.75    1.000
alpha{3}        4.404865    0.973416    2.613763    6.329489    4.291220   1159.58   1330.29    1.000
pinvar{all}     0.039734    0.000653    0.000042    0.087045    0.035043   1072.15   1161.00    1.001
------------------------------------------------------------------------------------------------------
* 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	-3340.425291
Model 2: PositiveSelection	-3340.425291
Model 0: one-ratio	-3356.040895
Model 3: discrete	-3314.907039
Model 7: beta	-3317.744351
Model 8: beta&w>1	-3317.619339


Model 0 vs 1	31.23120800000015

Model 2 vs 1	0.0

Model 8 vs 7	0.2500239999999394
>C1
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C2
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C3
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C4
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C5
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGoGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C6
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGKAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C7
SVSGDLILEIGKLPQHLTQKAQKALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C8
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C9
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C10
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLFWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C11
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEVGGKAYTHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C12
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C13
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C14
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C15
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C16
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSALLWMANV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C17
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C18
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C19
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C20
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C21
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C22
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEVGGKAYTHALSELPE
TLETLLLLTLLAAVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C23
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C24
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C25
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C26
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C27
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGoLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C28
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGVGKTSIGLICVVASSGMLWMADI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C29
SLTLSLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C30
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C31
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C32
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C33
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMSWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C34
SITLDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C35
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C36
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMSSSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C37
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C38
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C39
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C40
SLTLNIITEMGRLPTFMTQKTRDALDNLAVLHSAEMGGRAYNHALSELPE
TLETLLLLGLLATVTGGIFLFLMSGRGVGKMTLGMCCIITASGLLWYAQI
QPHWIAASIILEFFLTVLLIPEPEKQR
>C41
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C42
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C43
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C44
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASVLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C45
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C46
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHoAEMGGRAYNHALSELPE
TLETLLLLGLLATVTGGIFLFLMSGRGVGKMTLGMCCIITASGLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C47
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYKHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C48
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C49
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C50
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR

PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
-full_log      	S	[0] 
-genepred_score	S	[0] 	nsd
-run_name      	S	[0] 
-mem_mode      	S	[0] 	mem
-extend        	D	[1] 	1 
-extend_mode   	S	[0] 	very_fast_triplet
-max_n_pair    	D	[0] 	10 
-seq_name_for_quadruplet	S	[0] 	all
-compact       	S	[0] 	default
-clean         	S	[0] 	no
-do_self       	FL	[0] 	0
-do_normalise  	D	[0] 	1000 
-template_file 	S	[0] 
-setenv        	S	[0] 	0
-template_mode 	S	[0] 
-flip          	D	[0] 	0 
-remove_template_file	D	[0] 	0 
-profile_template_file	S	[0] 
-in            	S	[0] 
-seq           	S	[0] 
-aln           	S	[0] 
-method_limits 	S	[0] 
-method        	S	[0] 
-lib           	S	[0] 
-profile       	S	[0] 
-profile1      	S	[0] 
-profile2      	S	[0] 
-pdb           	S	[0] 
-relax_lib     	D	[0] 	1 
-filter_lib    	D	[0] 	0 
-shrink_lib    	D