T_Coffee is a multiple sequence alignment package. The version included with this distribution of Rocks is v3.84
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@rocks-168 ~]$ t_coffee /opt/Bio/t_coffee/example/sample_aln2.fasta PROGRAM: T-COFFEE (Version_3.84) -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] Mlalign_id_pair Mslow_pair -seq S [1] /opt/Bio/t_coffee/example/sample_aln2.fasta -aln S [0] -method S [0] ......... -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_thread S [0] -lib_list S [0] INPUT FILES Input File (M) lalign_id_pair Input File (M) slow_pair Input File (S) /opt/Bio/t_coffee/example/sample_aln2.fasta Format clustal_aln 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: idscore_pair_wise] [distance_matrix_mode: idscore] 1cms 1cms_1 identity= 19% score=190 1cms 2apr identity= 34% score=340 1cms 3app identity= 31% score=310 1cms 4ape identity= 29% score=290 ....... 3app 4pep identity= 34% score=340 4ape 4pep identity= 31% score=310 READ/MAKE LIBRARIES:[3] lalign_id_pair [method] [Submit Job][TOT= 15][ 0 %][ELAPSED TIME: 0 sec.][REMAINING TIME: -1073750336 sec.] [Submit Job][TOT= 15][100 %][ELAPSED TIME: 0 sec.][REMAINING TIME: 0 sec.] [Retrieve Job][TOT= 15][ 0 %][ELAPSED TIME: 0 sec.][REMAINING TIME: 6722352 sec.] [Retrieve Job][TOT= 15][100 %][ELAPSED TIME: 0 sec.][REMAINING TIME: 0 sec.] slow_pair [method] ....... Library Total Size: [5142] #### File Type= WEIGHT Format= tc_weight Name= no | NOT PRODUCED [WARNING:T-COFFEE:Version_3.84] WEIGHTED MODE:t_coffee 1cms 0.61 1cms_1 3.32 2apr 0.59 3app 0.49 4ape 0.48 4pep 0.51 MAKE NEIGHBOR JOINING DENDROGRAM [MODE=nj][DONE] PROGRESSIVE_ALIGNMENT [Tree Based] Group 7: [Group 6 ( 1 seq)] with [Group 1 ( 1 seq)]-->[Score= 53][Len= 176] Group 8: [Group 2 ( 1 seq)] with [Group 7 ( 2 seq)]-->[Score= 8][Len= 196] ...... CLUSTAL FORMAT for T-COFFEE Version_3.84, CPU=0.94 sec, SCORE=34, Nseq=6, Len=204 1cms ---gevasvpltnyl-dsqyfgkiylgtppqeftv------------------lfdtgss 4pep -----igdeplenyl-dteyfgtigigtpaqdftv------------------ifdtgss 1cms_1 y-tgslhwvpvtv----qqyw----------qftvdsvtisgvvvaceggcqaildtgts 2apr a---gvgtvpmtdygndieyygqvtigtpgkkfnl------------------dfdtgss 4ape s-tgsatttpids-l-ddayitpvqigtpaqtlnl------------------dfdtgss 3app aasgvatntptan---deeyitpvtig--gttlnl------------------nfdtgsa * * :.: :***:: ...... OUTPUT RESULTS #### File Type= GUIDE_TREE Format= newick Name= sample_aln2.dnd #### File Type= MSA Format= clustalw Name= sample_aln2.aln TIP: Change the Width of your MSA with the environement variable ALN_LINE_LENGTH (all formats) Command Line: t_coffee /opt/Bio/t_coffee/example/sample_aln2.fasta [PROGRAM:T-COFFEE] T-COFFEE Memory Usage: Current= 4.233 Mb, Max= 6.807 Mb T-COFFEE CPU Usage: 940 millisec [nostromo@rocks-168 ~]$ |
Further information about t_coffee is available at -
On your cluster head node at /opt/Bio/t_coffee/doc/