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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/
