2 PROGRAM: T-COFFEE (Version_8.14)
7 -extend_mode S [0] very_fast_triplet
9 -seq_name_for_quadruplet S [0] all
10 -compact S [0] default
13 -do_normalise D [0] 1000
16 -remove_template_file D [0] 0
17 -profile_template_file S [0]
32 -out_lib_mode S [0] primary
34 -outseqweight W_F [0] no
37 -cosmetic_penalty D [0] 0
43 -newtree W_F [0] default
47 -distance_matrix_mode S [0] ktup
48 -distance_matrix_sim_mode S [0] idmat_sim1
50 -outfile W_F [0] default
52 -output S [1] clustalw
56 -profile_mode S [0] cw_profile_profile
57 -profile_comparison S [0] profile
58 -dp_mode S [0] linked_pair_wise
61 -diag_threshold D [0] 0
63 -sim_matrix S [0] vasiliky
66 -inorder S [0] aligned
73 -seq_weight S [0] t_coffee
80 -mocca_interactive FL [0] 0
81 -method_evaluate_mode S [0] default
82 -evaluate_mode S [0] t_coffee_fast
85 -clean_threshold D [1] 1
86 -clean_iteration D [1] 1
87 -clean_evaluate_mode S [0] t_coffee_fast
88 -extend_matrix FL [0] 0
90 -prot_max_sim D [90] 90
92 -pdb_min_sim D [35] 35
93 -pdb_max_sim D [100] 100
94 -pdb_min_cov D [50] 50
95 -pdb_blast_server W_F [0] EBI
97 -blast_server W_F [0] EBI
99 -protein_db W_F [0] uniprot
100 -method_log W_F [0] no
103 -align_pdb_param_file W_F [0] no
104 -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble
105 -external_aligner S [0] NO
109 -lalign_n_top D [0] 10
113 -trimfile S [0] default
115 -split_nseq_thres D [0] 0
116 -split_score_thres D [0] 0
117 -check_pdb_status D [0] 0
118 -clean_seq_name D [0] 0
120 -dpa_master_aln S [0]
122 -dpa_min_score1 D [0]
123 -dpa_min_score2 D [0]
124 -dpa_keep_tmpfile FL [0] 0
126 -multi_core S [0] templates_jobs_relax_msa
129 -prune_lib_mode S [0] 5
133 -run_local_script D [0] 0
134 -plugins S [0] default
137 -clean_overaln D [0] 0
141 -overaln_threshold D [0] 0
142 -overaln_target D [0] 0
147 -exon_boundaries S [0]
150 Input File (S) fasta.in Format fasta_seq
151 Input File (M) proba_pair
153 INPUT SEQUENCES: 9 SEQUENCES [PROTEIN]
154 Input File fasta.in Seq Sequence0 Length 113 type PROTEIN Struct Unchecked
155 Input File fasta.in Seq Sequence1 Length 52 type PROTEIN Struct Unchecked
156 Input File fasta.in Seq Sequence2 Length 53 type PROTEIN Struct Unchecked
157 Input File fasta.in Seq Sequence3 Length 80 type PROTEIN Struct Unchecked
158 Input File fasta.in Seq Sequence4 Length 45 type PROTEIN Struct Unchecked
159 Input File fasta.in Seq Sequence5 Length 56 type PROTEIN Struct Unchecked
160 Input File fasta.in Seq Sequence6 Length 62 type PROTEIN Struct Unchecked
161 Input File fasta.in Seq Sequence7 Length 40 type PROTEIN Struct Unchecked
162 Input File fasta.in Seq Sequence8 Length 61 type PROTEIN Struct Unchecked
164 COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1]
176 READ/MAKE LIBRARIES:[2]
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217 MANUAL PENALTIES: gapopen=0 gapext=0
219 Library Total Size: [6542]
221 Library Relaxation:[6542] --->[5767]
223 #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14]
226 WEIGHTED MODE:t_coffee
242 PROGRESSIVE_ALIGNMENT [Tree Based]
244 Group 10: [Group 8 ( 1 seq)] with [Group 5 ( 1 seq)]-->[Score= 31][Len= 48][PID:23942]
245 Group 11: [Group 10 ( 2 seq)] with [Group 3 ( 1 seq)]-->[Score= 32][Len= 55][PID:23942]
246 Group 12: [Group 9 ( 1 seq)] with [Group 11 ( 3 seq)]-->[Score= 34][Len= 63][PID:23942]
247 Group 13: [Group 12 ( 4 seq)] with [Group 4 ( 1 seq)]-->[Score= 11][Len= 95][PID:23942]
248 Group 14: [Group 6 ( 1 seq)] with [Group 2 ( 1 seq)]-->[Score= 80][Len= 56][PID:23942]
249 Group 15: [Group 7 ( 1 seq)] with [Group 14 ( 2 seq)]-->[Score= 63][Len= 62][PID:23942]
250 Group 16: [Group 15 ( 3 seq)] with [Group 13 ( 5 seq)]-->[Score= 12][Len= 102][PID:23942]
251 Group 17: [Group 1 ( 1 seq)] with [Group 16 ( 8 seq)]-->[Score= 11][Len= 142][PID:23942]
256 #### File Type= GUIDE_TREE Format= newick Name= fasta.dnd
257 #### File Type= MSA Format= clustalw Name= fasta.clustalw
260 # TIP :See The Full Documentation on www.tcoffee.org
261 # TIP 1: Get the most accurate protein alignments with: t_coffee <yourseq> -special_mode accurate [Slow]
262 # TIP 10: -usetree=<file> to use your own guide tree
264 # Command Line: /homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee -output=clustalw -seq=fasta.in -n_core=1 [PROGRAM:T-COFFEE]
265 # T-COFFEE Memory Usage: Current= 11.932 Mb, Max= 13.916 Mb
266 # T-COFFEE CPU Usage: 250 millisec
267 # Results Produced with T-COFFEE (Version_8.14)
268 # T-COFFEE is available from http://www.tcoffee.org