T_Coffee is a multiple sequence alignment package. The version included with this distribution of Rocks is v5.65
T-coffee is used for standard alignments and alignment combinations. It is installed at /opt/Bio/t_coffee/ 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/t_coffee/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/t_coffee/example/sample_aln2.fasta PROGRAM: T-COFFEE (Version_5.65) -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] -in S [0] -seq S [1] /opt/Bio/t_coffee/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] -out_lib W_F [0] no -lib_only D [0] 0 -outseqweight W_F [0] no -dpa FL [0] 0 -seq_source S [0] ANY -cosmetic_penalty D [0] -50 -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] clustalw 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] cfasta_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] -check_type FL [0] 0 -type S [0] -outorder S [0] aligned -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 -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 [40] 40 -prot_max_sim D [60] 60 -prot_min_cov D [0] 0 -pdb_min_sim D [30] 30 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] SIB -prot_blast_server W_F [0] SIB -pdb_db W_F [0] nrl3d -protein_db W_F [0] nr -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] -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_thread S [0] -lib_list S [0] -tip S [0] one -rna_lib S [0] -no_warning D [0] 0 INPUT FILES Input File (S) /opt/Bio/t_coffee/example/sample_aln2.fasta Format clustal_aln Input File (M) lalign_id_pair Input File (M) slow_pair INPUT SEQUENCES: 6 SEQUENCES [PROTEIN] Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 1cms Length 175 type PROTEIN Struct Unchecked Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 4pep Length 174 type PROTEIN Struct Unchecked Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 4ape Length 178 type PROTEIN Struct Unchecked Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 3app Length 174 type PROTEIN Struct Unchecked Input File /opt/Bio/t_coffee/example/sample_aln2.fasta Seq 2apr Length 178 type PROTEIN Struct Unchecked Input File /opt/Bio/t_coffee/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:[3] lalign_id_pair [method] [Submit Job][TOT= 15][100 %][ELAPSED TIME: 0 sec.] [Retrieve Job][TOT= 15][100 %][ELAPSED TIME: 0 sec.] slow_pair [method] [Submit Job][TOT= 15][100 %][ELAPSED TIME: 0 sec.] [Retrieve Job][TOT= 15][100 %][ELAPSED TIME: 0 sec.] Library Total Size: [5133] #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_5.65] WEIGHTED MODE:t_coffee 1cms 1.00 1cms_1 1.10 2apr 1.00 3app 0.96 4ape 0.95 4pep 0.99 MAKE NEIGHBOR JOINING DENDROGRAM [MODE=nj][DONE] PROGRESSIVE_ALIGNMENT [Tree Based] Group 7: [Group 5 ( 1 seq)] with [Group 4 ( 1 seq)]-->[Score= 50][Len= 179] Group 8: [Group 7 ( 2 seq)] with [Group 6 ( 1 seq)]-->[Score= 36][Len= 184] Group 9: [Group 2 ( 1 seq)] with [Group 1 ( 1 seq)]-->[Score= 10][Len= 212] Group 10: [Group 3 ( 1 seq)] with [Group 9 ( 2 seq)]-->[Score= 26][Len= 217] Group 11: [Group 10 ( 3 seq)] with [Group 8 ( 3 seq)]-->[Score= 30][Len= 221] CLUSTAL FORMAT for T-COFFEE Version_5.65 [http://www.tcoffee.org], CPU=0.93 sec, SCORE=37, Nseq=6, Len=221 3app AASGVATNTPTAN---DEEYITPVTIG--GTTLNL------------------NFDTGSA 4ape -STGSATTTPIDS-L-DDAYITPVQIGTPAQTLNL------------------DFDTGSS 4pep -----IGDEPLENYL-DTEYFGTIGIGTPAQDFTV------------------IFDTGSS 1cms ---GEVASVPLTNYL-DSQYFGKIYLGTPPQEFTV------------------LFDTGSS 1cms_1 -YTGSLHWVPVT----VQQYW----------QFTVDSVTISGVVVACEGGCQAILDTGTS 2apr ---AGVGTVPMTDYGNDIEYYGQVTIGTPGKKFNL------------------DFDTGSS * * :.: :***:: 3app DLWVFSTELPASQQSGHSVYNPSATGK--ELSGYTWSISYGDGSSASGNVFTDSVTVGGV 4ape DLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYGDGSSSSGDVYTDTVSVGGL 4pep NLWVPSVYCSSLACSDHNQFNPDDSSTFEA-TSQELSITYGTGS-MTGILGYDTVQVGGI 1cms DFWVPSIYCKSNACKNHQRFDPRKSSTFQN-LGKPLSIHYGTGS-MQGILGYDTVTVSNI 1cms_1 KLVGPSSD---------------------------------------------------I 2apr DLWIASTLCTNCG-SGQTKYDPNQSSTYQA-DGRTWSISYGDGSSASGILAKDNVNLGGL .: * : 3app TAHGQAVQAAQQISAQFQQDTNNDG--------LLGLAFSSINTVQPQSQTT-------- 4ape TVTGQAVESAKKVSSSFTEDSTIDG--------LLGLAFSTLNTVSPTQQKT-------- 4pep SDTNQIFGLSETEPGSFLYYAPFDG--------ILGLAYPSISA---SGATP-------- 1cms VDIQQTVGLSTQEPGDVFTYAEFDG--------ILGMAYPSLASEYS---IP-------- 1cms_1 LNIQQAIGATQNQYGEFDIDCDNLSYMPTVVFEINGKMYPLTPSAYT---SQDQGFCTSG 2apr LIKGQTIELAKREAASFAS-GPNDG--------LLGLGFDTITTVRGV--KT-------- * . : ... . : * : : 3app -FFDTV--KSSLAQPLFAVALK---HQQPGVYDFGFIDSSK 4ape -FFDNA--KASLDSPVFTADLG---YHAPGTYNFGFIDTTA 4pep -VFDNLWDQGLVSQDLFSVYLS-SNDDSGSVVLLGGIDSSY 1cms -VFDNMMNRHLVAQDLFSVYMD--RNGQESMLTLGAIDPSY 1cms_1 FQSENHSQKWILGDVFIREYYS--VFDRANN--LVGLAKAI 2apr -PMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGYDSTK :. : : .: . : : OUTPUT RESULTS #### File Type= GUIDE_TREE Format= newick Name= sample_aln2.dnd #### File Type= MSA Format= clustalw Name= sample_aln2.aln #### File Type= MSA Format= html Name= sample_aln2.html # TIP :See The Full Documentation on www.tcoffee.org # TIP 15: -other_pg seq_reformat -in <aln> -action +trim %50 Will reduce the redundancy of your MSA # Command Line: t_coffee /opt/Bio/t_coffee/example/sample_aln2.fasta [PROGRAM:T-COFFEE] # T-COFFEE Memory Usage: Current= 6.248 Mb, Max= 8.329 Mb # T-COFFEE CPU Usage: 930 millisec # Results Produced with T-COFFEE (Version_5.65) # 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/t_coffee/doc/