--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Wed Jul 11 18:00:18 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_5/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3640.23         -3687.98
2      -3644.73         -3696.54
--------------------------------------
TOTAL    -3640.91         -3695.85
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_N3/NS4A_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_N3/NS4A_5/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_5/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         8.660519    0.425873    7.415099    9.950002    8.637009    871.99    904.50    1.000
r(A<->C){all}   0.026296    0.000067    0.010330    0.041692    0.025610    734.99    750.99    1.000
r(A<->G){all}   0.230779    0.000636    0.183561    0.280790    0.229800    487.96    636.72    1.000
r(A<->T){all}   0.069101    0.000159    0.043629    0.092383    0.068821    767.20    849.14    1.002
r(C<->G){all}   0.020215    0.000064    0.006139    0.036322    0.019709    673.52    692.84    1.000
r(C<->T){all}   0.608553    0.000916    0.549104    0.665695    0.609714    467.70    550.97    1.000
r(G<->T){all}   0.045056    0.000152    0.022955    0.070210    0.043772    656.27    743.29    1.000
pi(A){all}      0.312290    0.000257    0.282375    0.345205    0.311999    665.82    799.20    1.001
pi(C){all}      0.256535    0.000219    0.228497    0.285311    0.256350    723.94    756.83    1.000
pi(G){all}      0.228667    0.000205    0.201849    0.258041    0.228500    960.38    997.21    1.000
pi(T){all}      0.202508    0.000155    0.178528    0.226854    0.202268    770.90    800.62    1.000
alpha{1,2}      0.235506    0.000519    0.193694    0.280474    0.233565    862.70   1035.32    1.000
alpha{3}        4.670807    1.007795    2.890384    6.680660    4.577061   1139.25   1285.10    1.000
pinvar{all}     0.050783    0.000731    0.001602    0.101547    0.047719   1044.84   1175.30    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	-2873.240253
Model 2: PositiveSelection	-2872.958535
Model 0: one-ratio	-2889.737012
Model 3: discrete	-2851.251066
Model 7: beta	-2857.294719
Model 8: beta&w>1	-2857.295396


Model 0 vs 1	32.99351800000022

Model 2 vs 1	0.5634359999994558

Model 8 vs 7	0.0013539999999920838
>C1
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C2
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C3
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVIASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C4
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C5
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C6
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C7
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C8
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C9
oIALDLVTEIGRVPSoLoHRTRNoLDoLVMoHTSEoooRAYRHAVEEoPE
TMETLoLoGLMIoLTGGAMLFLISoKGIGKTSIGLICVIVSSGMLWMoDo
PLQWIAoAIVLEFFMMVoLIPEPEooR
>C10
SMTLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLIAIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLVPEPEKQR
>C11
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C12
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C13
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C14
SVSGDLILEIGKLPQHLTLKAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C15
SIALDLVTEIGRVPTHLAHRTRNALDNLVMLHTSEHGGKAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C16
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C17
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C18
SITLDILTEIASLPTYLSSRAKLAPDNIVMLHTTERGGKAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGMGKLSMGLIAIAVASGLLWVAEI
QPQWIAASIILEFFLMALLIPEPEKQR
>C19
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C20
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C21
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C22
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGKAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C23
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C24
SLTLSLITEMGRLPTFMTQKTRDALDNLAVLHSAEMGGRAYNHALSELPE
TLETLLLLGLLATVTGGIFLFLMSGRGVGKMTLGMCCIITASGLLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C25
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C26
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C27
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C28
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C29
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGVGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C30
SLTLNLITEMGRLPTFMTQKARNALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C31
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAAI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C32
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C33
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C34
SLTLNLITEMGRLPTFMTQKTRDALDNLAVLHTAEAGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIVTASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C35
SVSSDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETIMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVTSSSALLWMANV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C36
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C37
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEAGGKAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGRGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C38
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLVLIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C39
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C40
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMGSV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C41
SLTLNLITEMGRLPTFMTQKARDALDNLAVLHTAEVGGRAYNHALSELPE
TLETLLLLTLLATVTGGIFLFLMSGKGIGKMTLGMCCIITASILLWYAQI
QPHWIAASIILEFFLIVLLIPEPEKQR
>C42
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMSWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C43
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C44
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C45
SITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRAYQHALNELPE
SLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVAEI
QPQWIAASIILEFFLMVLLIPEPEKQR
>C46
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVMASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C47
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIASSGMLWMAEI
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C48
SVSGDLILEIGKLPQHLTLRAQNALDNLVMLHNSEQGGKAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGKGLGKTSIGLLCVTASSALLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR
>C49
SIALDLVTEIGRVPSHLAHRTRNALDNLVMLHTSEHGGRAYRHAVEELPE
TMETLLLLGLMILLTGGAMLFLISGKGIGKTSIGLICVIVSSGMLWMADV
PLQWIASAIVLEFFMMVLLIPEPEKQR
>C50
SVSGDLILEIGKLPQHLTQRAQNALDNLVMLHNSEQGGRAYRHAMEELPD
TIETLMLLALIAVLTGGVTLFFLSGRGLGKTSIGLLCVIASSVLLWMASV
EPHWIAASIILEFFLMVLLIPEPDRQR

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	[0] 	0 
-out_lib       	W_F	[0] 	no
-out_lib_mode  	S	[0] 	primary
-lib_only      	D	[0] 	0 
-outseqweight  	W_F	[0] 	no
-dpa           	FL	[0] 	0
-seq_source    	S	[0] 	ANY
-cosmetic_penalty	D	[0] 	0 
-gapopen       	D	[0] 	0 
-gapext        	D	[0] 	0 
-fgapopen      	D	[0] 	0 
-fgapext       	D	[0] 	0 
-nomatch       	D	[0] 	0 
-newtree       	W_F	[0] 	default
-tree          	W_F	[0] 	NO
-usetree       	R_F	[0] 
-tree_mode     	S	[0] 	nj
-distance_matrix_mode	S	[0] 	ktup
-distance_matrix_sim_mode	S	[0] 	idmat_sim1
-quicktree     	FL	[0] 	0
-outfile       	W_F	[0] 	default
-maximise      	FL	[1] 	1
-output        	S	[1] 	score_ascii	html	score_ascii
-len           	D	[0] 	0 
-infile        	R_F	[1] 	input.prot.fasta.muscle_rs_0_0.fasta.aln
-matrix        	S	[0] 	default
-tg_mode       	D	[0] 	1 
-profile_mode  	S	[0] 	cw_profile_profile
-profile_comparison	S	[0] 	profile
-dp_mode       	S	[0] 	linked_pair_wise
-ktuple        	D	[0] 	1 
-ndiag         	D	[0] 	0 
-diag_threshold	D	[0] 	0 
-diag_mode     	D	[0] 	0 
-sim_matrix    	S	[0] 	vasiliky
-transform     	S	[0] 
-extend_seq    	FL	[0] 	0
-outorder      	S	[0] 	input
-inorder       	S	[0] 	aligned
-seqnos        	S	[0] 	off
-case          	S	[0] 	keep
-cpu           	D	[0] 	0 
-maxnseq       	D	[0] 	1000 
-maxlen        	D	[0] 	-1 
-sample_dp     	D	[0] 	0 
-weight        	S	[0] 	default
-seq_weight    	S	[0] 	no
-align         	FL	[1] 	1
-mocca         	FL	[0] 	0
-domain        	FL	[0] 	0
-start         	D	[0] 	0 
-len           	D	[0] 	0 
-scale         	D	[0] 	0 
-mocca_interactive	FL	[0] 	0
-method_evaluate_mode	S	[0] 	default
-evaluate_mode 	S	[1] 	t_coffee_fast
-get_type      	FL	[0] 	0
-clean_aln     	D	[0] 	0 
-clean_threshold	D	[1] 	1 
-clean_iteration	D	[1] 	1 
-clean_evaluate_mode	S	[0] 	t_coffee_fast
-extend_matrix 	FL	[0] 	0
-prot_min_sim  	D	[40] 	40 
-prot_max_sim  	D	[90] 	90 
-prot_min_cov  	D	[40] 	40 
-pdb_type      	S	[0] 	d
-pdb_min_sim   	D	[35] 	35 
-pdb_max_sim   	D	[100] 	100 
-pdb_min_cov   	D	[50] 	50 
-pdb_blast_server	W_F	[0] 	EBI
-blast         	W_F	[0] 
-blast_server  	W_F	[0] 	EBI
-pdb_db        	W_F	[0] 	pdb
-protein_db    	W_F	[0] 	uniprot
-method_log    	W_F	[0] 	no
-struc_to_use  	S	[0] 
-cache         	W_F	[0] 	use
-align_pdb_param_file	W_F	[0] 	no
-align_pdb_hasch_mode	W_F	[0] 	hasch_ca_trace_bubble
-external_aligner	S	[0] 	NO
-msa_mode      	S	[0] 	tree
-master        	S	[0] 	no
-blast_nseq    	D	[0] 	0 
-lalign_n_top  	D	[0] 	10 
-iterate       	D	[1] 	0 
-trim          	D	[0] 	0 
-split         	D	[0] 	0 
-trimfile      	S	[0] 	default
-split         	D	[0] 	0 
-split_nseq_thres	D	[0] 	0 
-split_score_thres	D	[0] 	0 
-check_pdb_status	D	[0] 	0 
-clean_seq_name	D	[0] 	0 
-seq_to_keep   	S	[0] 
-dpa_master_aln	S	[0] 
-dpa_maxnseq   	D	[0] 	0 
-dpa_min_score1	D	[0] 
-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.