PROGRAM: T-COFFEE (Version_8.14) -full_log S [0] -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] -template_mode S [0] -remove_template_file D [0] 0 -profile_template_file S [0] -in S [0] -seq S [1] fasta.in -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] clustalw -infile R_F [0] -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] -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 -weight S [0] default -seq_weight S [0] t_coffee -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 [0] 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 [0] 0 -prot_max_sim D [90] 90 -prot_min_cov D [0] 0 -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 -one2all S [0] -subset2all S [0] -lalign_n_top D [0] 10 -iterate D [0] 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 -n_core D [1] 4 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] one -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] INPUT FILES Input File (S) fasta.in Format fasta_seq Input File (M) proba_pair INPUT SEQUENCES: 10 SEQUENCES [PROTEIN] Input File fasta.in Seq Sequence0 Length 313 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence1 Length 965 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence2 Length 492 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence3 Length 1057 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence4 Length 577 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence5 Length 1124 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence6 Length 794 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence7 Length 326 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence8 Length 402 type PROTEIN Struct Unchecked Input File fasta.in Seq Sequence9 Length 482 type PROTEIN Struct Unchecked COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1] Seq: Sequence0 Seq: Sequence1 Seq: Sequence2 Seq: Sequence3 Seq: Sequence4 Seq: Sequence5 Seq: Sequence6 Seq: Sequence7 Seq: Sequence8 Seq: Sequence9 READ/MAKE LIBRARIES:[2] proba_pair [method] Multi Core Mode: 4 processors [subset] [Submit Job][TOT= 12][ 0 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 16 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 25 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 33 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 41 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 50 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 58 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 66 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 75 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 83 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT= 12][ 91 %][ELAPSED TIME: 1 sec.] [Submit Job][TOT= 12][100 %][ELAPSED TIME: 1 sec.] MANUAL PENALTIES: gapopen=0 gapext=0 Library Total Size: [83014] Library Relaxation: Multi_proc [4] [Submit Job][TOT=20753][ 0 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 1 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 2 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 3 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 4 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 5 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 6 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 7 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 8 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 9 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 10 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 11 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 12 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 13 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 14 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 15 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 16 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 17 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 18 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 19 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 20 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 21 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 22 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 23 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 24 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 25 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 26 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 27 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 28 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 29 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 30 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 31 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 32 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 33 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 34 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 35 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 36 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 37 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 38 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 39 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 40 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 41 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 42 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 43 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 44 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 45 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 46 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 47 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 48 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 49 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 50 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 51 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 52 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 53 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 54 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 55 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 56 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 57 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 58 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 59 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 60 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 61 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 62 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 63 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 64 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 65 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 66 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 67 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 68 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 69 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 70 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 71 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 72 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 73 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 74 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 75 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 76 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 77 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 78 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 79 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 80 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 81 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 82 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 83 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 84 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 85 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 86 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 87 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 88 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 89 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 90 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 91 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 92 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 93 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 94 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 95 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 96 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 97 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 98 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][ 99 %][ELAPSED TIME: 0 sec.] [Submit Job][TOT=20753][100 %][ELAPSED TIME: 0 sec.] Total Relaxation: [83014]--->[53572] Entries #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14] WEIGHTED MODE:t_coffee Sequence0 1.05 Sequence1 1.01 Sequence2 1.00 Sequence3 0.93 Sequence4 1.06 Sequence5 0.98 Sequence6 0.94 Sequence7 0.99 Sequence8 1.05 Sequence9 1.00 MAKE GUIDE TREE [MODE=nj][DONE] PROGRESSIVE_ALIGNMENT [Tree Based] Group 13: [Group 8 ( 1 seq)] with [Group 6 ( 1 seq)]-->[Score= 2][Len= 1157][PID:29128] Group 11: [Group 7 ( 1 seq)] with [Group 4 ( 1 seq)]-->[Score= 27][Len= 1083][PID:29126] Group 14: [Group 10 ( 1 seq)] with [Group 13 ( 2 seq)]-->[Score= 4][Len= 1173][PID:29128] Group 12: [Group 11 ( 2 seq)] with [Group 3 ( 1 seq)]-->[Score= 8][Len= 1123][PID:29126] Group 15: [Group 14 ( 3 seq)] with [Group 2 ( 1 seq)]-->[Score= 13][Len= 1239][PID:29128] Group 17: [Group 16 ( 2 seq)] with [Group 15 ( 4 seq)]-->[Score= 2][Len= 1262][PID:29127][Forked] Group 18: [Group 17 ( 6 seq)] with [Group 12 ( 3 seq)]-->[Score= 4][Len= 1612][PID:29108][Forked] Group 19: [Group 5 ( 1 seq)] with [Group 18 ( 9 seq)]-->[Score= 3][Len= 1655][PID:29108] OUTPUT RESULTS #### File Type= GUIDE_TREE Format= newick Name= fasta.dnd #### File Type= MSA Format= clustalw Name= fasta.clustalw # TIP :See The Full Documentation on www.tcoffee.org # TIP 1: Get the most accurate protein alignments with: t_coffee -special_mode accurate [Slow] # TIP 2: Change the Width of your MSA with the environement variable ALN_LINE_LENGTH (all formats) # 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=4 [PROGRAM:T-COFFEE] # T-COFFEE Memory Usage: Current= 19.700 Mb, Max= 28.281 Mb # T-COFFEE CPU Usage: 10 millisec # Results Produced with T-COFFEE (Version_8.14) # T-COFFEE is available from http://www.tcoffee.org