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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/
