--- /dev/null
+
+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] 1
+-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: 9 SEQUENCES [PROTEIN]
+ Input File fasta.in Seq Sequence0 Length 113 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence1 Length 52 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence2 Length 53 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence3 Length 80 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence4 Length 45 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence5 Length 56 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence6 Length 62 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence7 Length 40 type PROTEIN Struct Unchecked
+ Input File fasta.in Seq Sequence8 Length 61 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
+
+READ/MAKE LIBRARIES:[2]
+
+ proba_pair [method]
+
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+ [Submit Job][TOT= 36][100 %][ELAPSED TIME: 0 sec.]
+
+MANUAL PENALTIES: gapopen=0 gapext=0
+
+ Library Total Size: [6542]
+
+Library Relaxation:[6542] --->[5767]
+
+ #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14]
+
+
+WEIGHTED MODE:t_coffee
+
+ Sequence0 1.08
+ Sequence1 0.82
+ Sequence2 1.07
+ Sequence3 1.08
+ Sequence4 1.05
+ Sequence5 0.82
+ Sequence6 0.95
+ Sequence7 1.05
+ Sequence8 1.07
+
+
+MAKE GUIDE TREE
+ [MODE=nj][DONE]
+
+PROGRESSIVE_ALIGNMENT [Tree Based]
+
+ Group 10: [Group 8 ( 1 seq)] with [Group 5 ( 1 seq)]-->[Score= 31][Len= 48][PID:23942]
+ Group 11: [Group 10 ( 2 seq)] with [Group 3 ( 1 seq)]-->[Score= 32][Len= 55][PID:23942]
+ Group 12: [Group 9 ( 1 seq)] with [Group 11 ( 3 seq)]-->[Score= 34][Len= 63][PID:23942]
+ Group 13: [Group 12 ( 4 seq)] with [Group 4 ( 1 seq)]-->[Score= 11][Len= 95][PID:23942]
+ Group 14: [Group 6 ( 1 seq)] with [Group 2 ( 1 seq)]-->[Score= 80][Len= 56][PID:23942]
+ Group 15: [Group 7 ( 1 seq)] with [Group 14 ( 2 seq)]-->[Score= 63][Len= 62][PID:23942]
+ Group 16: [Group 15 ( 3 seq)] with [Group 13 ( 5 seq)]-->[Score= 12][Len= 102][PID:23942]
+ Group 17: [Group 1 ( 1 seq)] with [Group 16 ( 8 seq)]-->[Score= 11][Len= 142][PID:23942]
+
+
+
+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 <yourseq> -special_mode accurate [Slow]
+# TIP 10: -usetree=<file> to use your own guide tree
+
+# 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]
+# T-COFFEE Memory Usage: Current= 11.932 Mb, Max= 13.916 Mb
+# T-COFFEE CPU Usage: 250 millisec
+# Results Produced with T-COFFEE (Version_8.14)
+# T-COFFEE is available from http://www.tcoffee.org
git://source.jalview.org / jabaws.git / blobdiff