--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Mon Oct 31 19:46:03 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
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/ADOPS/128/CG34136-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/128/CG34136-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/128/CG34136-PA/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/ADOPS/128/CG34136-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1       -754.58          -770.94
2       -755.00          -768.95
--------------------------------------
TOTAL     -754.77          -770.38
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/128/CG34136-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/128/CG34136-PA/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/ADOPS/128/CG34136-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         1.307742    0.047509    0.915263    1.745533    1.290413   1256.47   1378.73    1.000
r(A<->C){all}   0.155407    0.002582    0.065043    0.256972    0.151876    573.62    664.92    1.003
r(A<->G){all}   0.237986    0.004746    0.117070    0.375971    0.230027    527.79    663.48    1.001
r(A<->T){all}   0.101513    0.002006    0.021453    0.187784    0.096931    838.97    844.86    1.003
r(C<->G){all}   0.025833    0.000314    0.000015    0.059717    0.022725    967.44    994.91    1.000
r(C<->T){all}   0.450892    0.006478    0.282467    0.595929    0.451552    551.36    554.72    1.001
r(G<->T){all}   0.028368    0.000342    0.000009    0.064008    0.024809    668.99    879.63    1.002
pi(A){all}      0.226339    0.000622    0.176831    0.273778    0.225487    896.00   1106.35    1.000
pi(C){all}      0.266336    0.000708    0.210521    0.315732    0.265825    732.94    845.64    1.000
pi(G){all}      0.250408    0.000721    0.199227    0.304458    0.250191    908.79   1204.89    1.000
pi(T){all}      0.256916    0.000688    0.204267    0.306279    0.256460   1094.34   1116.63    1.000
alpha{1,2}      0.107439    0.000545    0.069203    0.156872    0.104910   1354.59   1362.35    1.000
alpha{3}        1.831512    0.450959    0.721324    3.178297    1.717340   1342.80   1421.90    1.000
pinvar{all}     0.379773    0.007002    0.207156    0.534650    0.384286   1170.89   1228.97    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	-703.835402
Model 2: PositiveSelection	-703.835402
Model 0: one-ratio	-704.164499
Model 3: discrete	-702.971495
Model 7: beta	-703.021233
Model 8: beta&w>1	-703.021493


Model 0 vs 1	0.6581939999998667

Model 2 vs 1	0.0

Model 8 vs 7	5.199999998239946E-4
>C1
MWPNFLAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C2
MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C3
MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C4
MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C5
MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C6
MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C7
MWPNFVAVISLLCLAFFAWANAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C8
MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C9
MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C10
MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C11
MWPNFVAVFSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
>C12
MWPNFVAVISMLCLAFFTWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
VLMMRRCRHLRVPTAPRLGDVLKRKKK
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=12, Len=77 

C1              MWPNFLAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C2              MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C3              MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C4              MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C5              MWPNFVAVVSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C6              MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C7              MWPNFVAVISLLCLAFFAWANAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C8              MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C9              MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C10             MWPNFVAVISLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C11             MWPNFVAVFSLLCLAFFAWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
C12             MWPNFVAVISMLCLAFFTWAKAGPVPIVNEHQQLMPKVPQWHCLRYFKHD
                *****:**.*:******:**:*****************************

C1              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C2              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C3              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C4              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C5              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C6              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C7              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C8              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C9              VLMMRRCRHLRVPTAPRLGDVLKRKKK
C10             VLMMRRCRHLRVPTAPRLGDVLKRKKK
C11             VLMMRRCRHLRVPTAPRLGDVLKRKKK
C12             VLMMRRCRHLRVPTAPRLGDVLKRKKK
                ***************************




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] 	/opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C12 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length   77 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:
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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C12 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length   77 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C12 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length   77 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C12 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length   77 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C12 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length   77 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C12 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length   77 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnplugins       	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) /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 12 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length   77 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/128/CG34136-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clus