--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Jun 01 22:17:02 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_A1/NS2B_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A1/NS2B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS2B_2/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_A1/NS2B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4028.13         -4070.10
2      -4026.17         -4071.82
--------------------------------------
TOTAL    -4026.73         -4071.29
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A1/NS2B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A1/NS2B_2/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_A1/NS2B_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         7.107565    0.288218    6.110475    8.211834    7.070084   1035.36   1060.76    1.000
r(A<->C){all}   0.069804    0.000136    0.046215    0.091549    0.069147    704.57    817.45    1.001
r(A<->G){all}   0.233700    0.000599    0.190221    0.283874    0.233110    506.93    539.09    1.000
r(A<->T){all}   0.059876    0.000127    0.038825    0.081925    0.059499    808.40    860.44    1.000
r(C<->G){all}   0.046164    0.000122    0.026560    0.069557    0.045426    753.31    837.11    1.000
r(C<->T){all}   0.554024    0.000969    0.492999    0.613590    0.553923    508.81    520.69    1.000
r(G<->T){all}   0.036432    0.000091    0.017427    0.054539    0.035681    930.57    992.69    1.000
pi(A){all}      0.317266    0.000249    0.287296    0.349006    0.317439    885.20    991.26    1.000
pi(C){all}      0.219754    0.000181    0.194416    0.245452    0.219293    953.23    980.99    1.000
pi(G){all}      0.240856    0.000205    0.212871    0.268755    0.240808    629.75    723.88    1.000
pi(T){all}      0.222124    0.000186    0.194402    0.248038    0.222086    747.66    774.03    1.000
alpha{1,2}      0.280620    0.001055    0.220697    0.342800    0.278100   1117.85   1174.90    1.002
alpha{3}        3.933918    0.821003    2.276941    5.743397    3.812010   1501.00   1501.00    1.000
pinvar{all}     0.053898    0.000619    0.007496    0.100735    0.052471   1200.86   1318.30    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	-3847.664429
Model 2: PositiveSelection	-3847.664429
Model 0: one-ratio	-3872.217263
Model 3: discrete	-3824.299285
Model 7: beta	-3829.663625
Model 8: beta&w>1	-3825.61521


Model 0 vs 1	49.10566800000015

Model 2 vs 1	0.0

Model 8 vs 7	8.09683000000041

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: gb:JF920409|Organism:Dengue_virus_3|Strain_Name:DENV-3/NI/BID-V5471/2010|Protein_Name:Nonstructural_protein_NS2B|Gene_Symbol:NS2b)

            Pr(w>1)     post mean +- SE for w


>C1
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADITWEEEAEQTGVSHNLMITVDDDGTMRIKDDESENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C2
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLISFFVISGSSAD
LSLEKAAEVSWEEEAEHSGTSHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C3
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADIIWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C4
SWPLNEGVMAIGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETEHILTVLFK
TALLIVSGVFPYSIPATLLVWHTWQKQTQR
>C5
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVRWEEQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPASIPITAAAWYLWEVKKQR
>C6
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVKWDDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TELLVISGLFPISIPITAAAWYLWEVKKQR
>C7
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPLSIPATLFVWCFWQKKKQR
>C8
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADITWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLVVSGVFPYSIPATLLVWHTWQKQTQR
>C9
SWPLNEAIMAVGMVSILASSFLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADIRWEEQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPVSIPITAAAWYLWEVKKQR
>C10
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTTLLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C11
SWPLNEAVMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEHTLTILIR
TGLLVISGVFPLSIPITAAAWYLWEVKKQR
>C12
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDIEETNMITLLVK
LALITVSGLYPLAIPVTMTLWYMWQVKTQR
>C13
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADITWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C14
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADITWEEEAEQTGVSHNLTITVDDDGTMRIKDDETENILTVLLK
TALLIVSGVFPYSIPATLLVWHTWQKQTQR
>C15
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERATDVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPMSIPITAAAWYLWEVKKQR
>C16
SWPLNEAVMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELEKAADVRWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPISIPITAAAWYLWEVKKQR
>C17
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLERAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVK
LALITVSGLYPLAIPITMTLWYMWQVRTQR
>C18
SWPLNEGIMAVGIVSILLSSFLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGMYPLSIPATLFVWYFWQKKKQR
>C19
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLVAGGMLIACYVISGSSAD
LSLEKAAEVSWEQEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C20
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEVEHSGTSHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C21
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIQDVEETNMITLLVK
LALITVSGLYPLAIPVTMTLWYMWQVKTQR
>C22
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEQEAEHSGTSHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKRKQR
>C23
SWPLNEGIMAVGVVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPLSIPATLFVWHFWQKKKQR
>C24
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELEKAADVRWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPVSIPITAAAWYLWEVKKQR
>C25
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAQHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C26
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVK
LALITVSGLYPLAIPVTMALWYVWQVKTQR
>C27
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEQEAEHSGASHSILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQRKKQR
>C28
SWPLNEAIMAVGMVSILASSLLENDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVRWEDQAEISGSSPILSITISEDGSMSIKYEEEEPTLTILIR
TGLLVISGLFPVSIPITAAAWYLWEVKKQR
>C29
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEQEAEHSGTSHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C30
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPCSIPATLLVWHTWQKQTQR
>C31
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAVVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C32
SWPLNEAIMAVGMVSILASSFLKDDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADIRWEEQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPVSIPITAAAWYLWEVKKQR
>C33
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERATNVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPISIPITAAAWYLWEVKKQR
>C34
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELEKAADVRWEEQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPVSIPITAAAWYLWEVKKQR
>C35
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLEKAANVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVK
LALITVSGLYPLAIPVTMTLWYIWQVKTQR
>C36
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLERAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C37
SWPLNEGIMAVGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGPMKIKDEERDDMLTILLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C38
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGTSHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR
>C39
SWPLNEAIMAVGMVSILASSLLKDDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERATDVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGLFPISIPITAAAWYLWEVKKQR
>C40
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKRTQR
>C41
SWSLNEGVMAVGLVSILASSLLRNDVPMAGRLVAGGLLVGCYVITGTSSD
LTVEKAADVTCEEEAEQTGASHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C42
SWPLNEGIMAVGVVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C43
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVKWEDQAEVSGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGVFPVSIPITAAAWYLWEVKKQR
>C44
SWPLNEGIMAVGIVSILLSALLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEEEAEHSGGSHNILVEVQDDGTMKIKDEERDATLTILLK
ATLLAVSGVYPLSIPATLFVWYFWQKKKQR
>C45
SWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQILTILIR
TGLLVISGLFPVSIPITAAAWCLWEVKKQR
>C46
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LAVEKAADVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C47
IGPLNEAVMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSAD
LELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIR
TGLLVISGVFPVSIPITAAAWYLWEVKKQR
>C48
SWPLNEGVMAVGLVSILASSLLRNDVPMAGPLVAGGLLIACYVITGTSAD
LTVEKAANVTWEEEAEQTGVSHNLMITVDDDGTMRIKDDETENILTVLLK
TALLIVSGIFPYSIPATLLVWHTWQKQTQR
>C49
SWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVAGGLLLAAYVMSGSSAD
LSLEKAASVQWDEMADITGSSPIIEVKQDEDGSFSIRDVEETNMITLLVK
LALITVSGLYPLAIPVTMTLWYMWQVKTQR
>C50
SWPLNEGIMAIGIVSILLSSLLKNDVPLAGPLIAGGMLIACYVISGSSAD
LSLEKAAEVSWEQEAEHSGASHNILVEVQDDGTMKIKDEERDDTLTILLK
ATLLAVSGVYPMSIPATLFVWYFWQKKKQR

PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
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-do_normalise  	D	[0] 	1000 
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-setenv        	S	[0] 	0
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-output        	S	[1] 	score_ascii	html	score_ascii
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-infile        	R_F	[1] 	input.prot.fasta.muscle_rs_0_0.fasta.aln
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-prot_max_sim  	D	[90] 	90 
-prot_min_cov  	D	[40] 	40 
-pdb_type      	S	[0] 	d
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-pdb_max_sim   	D	[100] 	100 
-pdb_min_cov   	D	[50] 	50 
-pdb_blast_server	W_F	[0] 	EBI
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-blast_server  	W_F	[0] 	EBI
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-external_aligner	S	[0] 	NO
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-dpa_min_score2	D	[0] 
-dpa_keep_tmpfile	FL	[0] 	0
-dpa_debug     	D	[0] 	0 
-multi_core    	S	[0] 	templates_jobs_relax_msa_evaluate
-n_core        	D	[0] 	0 
-max_n_proc    	D	[0] 	0 
-lib_list      	S	[0] 
-prune_lib_mode	S	[0] 	5
-tip           	S	[0] 	none
-rna_lib       	S	[0] 
-no_warning    	D	[0] 	0 
-run_local_script	D	[0] 	0 
-plugins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-o