T_Coffee is a multiple sequence alignment package. The version included with this distribution of Rocks is v8.14
T-coffee is used for standard alignments and alignment combinations. It is installed at /opt/bio/tcoffee/ on the Rocks distribution. To use T-Coffee, just type t_coffee at the command line for a list of all possible parameters that can be used. T-coffee recognizes formats such as fasta, clustalw, blast, etc. Example input files are available at /opt/bio/tcoffee/example/
A simple sequence alignment example is shown below about. It is run against a sample fasta file present in the example directory. Parts of the output are deleted for the sake of brevity. Where missing, output is substituted by ellipses (.....)
[nostromo@xxx ~]$ t_coffee /opt/bio/tcoffee/example/sample_aln2.fasta 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] /opt/bio/tcoffee/example/sample_aln2.fasta -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 [0] aln html -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 [0] 0 -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) /opt/bio/tcoffee/example/sample_aln2.fasta Format clustal_aln Input File (M) proba_pair INPUT SEQUENCES: 6 SEQUENCES [PROTEIN] Input File /opt/bio/tcoffee/example/sample_aln2.fasta Seq 1cms Length 175 type PROTEIN Struct Unchecked Input File /opt/bio/tcoffee/example/sample_aln2.fasta Seq 4pep Length 174 type PROTEIN Struct Unchecked Input File /opt/bio/tcoffee/example/sample_aln2.fasta Seq 4ape Length 178 type PROTEIN Struct Unchecked Input File /opt/bio/tcoffee/example/sample_aln2.fasta Seq 3app Length 174 type PROTEIN Struct Unchecked Input File /opt/bio/tcoffee/example/sample_aln2.fasta Seq 2apr Length 178 type PROTEIN Struct Unchecked Input File /opt/bio/tcoffee/example/sample_aln2.fasta Seq 1cms_1 Length 148 type PROTEIN Struct Unchecked COMPUTE PAIRWISE SIMILARITY [dp_mode: ] [distance_matrix_mode: ktup][Similarity Measure: idmat_sim1] Seq: 1cms Seq: 1cms_1 Seq: 2apr Seq: 3app Seq: 4ape Seq: 4pep READ/MAKE LIBRARIES:[2] proba_pair [method] Multi Core Mode: 2 processors [subset] [Submit Job][TOT= 8][100 %][ELAPSED TIME: 0 sec.] MANUAL PENALTIES: gapopen=0 gapext=0 Library Total Size: [6175] Library Relaxation: Multi_proc [2] [Submit Job][TOT= 3087][100 %][ELAPSED TIME: 0 sec.] Total Relaxation: [6175]--->[5092] Entries #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_8.14] WEIGHTED MODE:t_coffee 1cms 1.00 1cms_1 1.10 2apr 1.00 3app 0.96 4ape 0.95 4pep 0.99 MAKE GUIDE TREE [MODE=nj][DONE] PROGRESSIVE_ALIGNMENT [Tree Based] Group 8: [Group 5 ( 1 seq)] with [Group 4 ( 1 seq)]-->[Score= 83][Len= 179][PID:17999] Group 7: [Group 6 ( 1 seq)] with [Group 1 ( 1 seq)]-->[Score= 92][Len= 176][PID:17998] Group 9: [Group 8 ( 2 seq)] with [Group 3 ( 1 seq)]-->[Score= 74][Len= 186][PID:17999] Group 10: [Group 9 ( 3 seq)] with [Group 7 ( 2 seq)]-->[Score= 77][Len= 186][PID:17976][Forked] Group 11: [Group 2 ( 1 seq)] with [Group 10 ( 5 seq)]-->[Score= 24][Len= 209][PID:17976] CLUSTAL FORMAT for T-COFFEE Version_8.14 [http://www.tcoffee.org] [MODE: ], CPU=0.15 sec, SCORE=72, Nseq=6, Len=209 1cms GE---VASVPLTNY------LDSQYFGKIYLGTPPQEFTVLFDTGSSDFWVPSIYCKSNA 4pep -----IGDEPLENY------LDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLA 4ape S-TGSATTTPID-S------LDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASE 3app AASGVATNTPTA--------NDEEYITPVTIGG--TTLNLNFDTGSADLWVFSTELPASQ 2apr AG---VGTVPMTDY-----GNDIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTN-C 1cms_1 Y-TGSLHWVPVTVQQYWQFTVDSVTISGVVVACEG-GCQAILDTGTSKLVGPSSD----- * * : :. :***::.: * 1cms CKNHQRFDPRKSSTFQ-NLGKPLSIHYGTGS-MQGILGYDTVTVSNIVDIQQTVGLSTQE 4pep CSDHNQFNPDDSSTFE-ATSQELSITYGTGS-MTGILGYDTVQVGGISDTNQIFGLSETE 4ape VDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGLTVTGQAVESAKKV 3app QSGHSVYNPSATG-KE-LSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQI 2apr GSGQTKYDPNQSSTYQ-ADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKRE 1cms_1 ----------------------------------------------ILNIQQAIGATQNQ : * . : 1cms PGDVFTYAEFD--------GILGMAYPSLASEY-------SIPVFDNM-MNRHLVA---- 4pep PGSFLYYAPFD--------GILGLAYPSISASG-------ATPVFDNL-WDQGLVS---- 4ape SSSFTEDSTID--------GLLGLAFSTLNTVSPTQ----QKTFFDNA---KASLD---- 3app SAQFQQDTNND--------GLLGLAFSSINTVQPQS----QTTFFDTV---KSSLA---- 2apr AASFAS-GPND--------GLLGLGFDTITTVRG------VKTPMDNL-ISQGLIS---- 1cms_1 YGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYTSQDQGFCTSGFQSENHSQKWILGDVF ... : * : : . ::. : : 1cms -QDLFSVYMDRN-G-QESMLTLGAIDPSY 4pep -QDLFSVYLSSN-DDSGSVVLLGGIDSSY 4ape -SPVFTADLGY---HAPGTYNFGFIDTTA 3app -QPLFAVALKH---QQPGVYDFGFIDSSK 2apr -RPIFGVYLGKAKNGGGGEYIFGGYDSTK 1cms_1 IREYYSVFDR--------ANNLVGLAKAI : . : : OUTPUT RESULTS #### File Type= GUIDE_TREE Format= newick Name= sample_aln2.dnd #### File Type= MSA Format= aln Name= sample_aln2.aln #### File Type= MSA Format= html Name= sample_aln2.html # 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 4: -special_mode=expresso to fetch your structures automatically # Command Line: t_coffee /opt/bio/tcoffee/example/sample_aln2.fasta [PROGRAM:T-COFFEE] # T-COFFEE Memory Usage: Current= 11.819 Mb, Max= 13.181 Mb # T-COFFEE CPU Usage: 160 millisec # Results Produced with T-COFFEE (Version_8.14) # T-COFFEE is available from http://www.tcoffee.org |
Further information about t_coffee is available at -
On your cluster head node at /opt/bio/tcoffee/doc/