Difference between revisions of "T-Coffee"
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| − | '''T-Coffee''' (Tree-based | + | '''T-Coffee''' ('''Tree-'''based '''C'''onsistency '''O'''bjective '''F'''unction '''F'''or alignm'''e'''nt '''E'''valuation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from [[Protein Data Bank|PDB]] files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity of identifying occurrence of motifs (Mocca). It produces alignment in the aln format ([[Clustal]]) by default, but can also produce PIR, MSF and FASTA format. The input files are always in [[FASTA format]]. Note that what T-Coffee terms "Clustal" format is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX ''can'' import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export. |
==Usage== | ==Usage== | ||
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*[[Clustal]] | *[[Clustal]] | ||
*[http://wikiomics.org/wiki/Bioinfo_tutorial Bioinfo tutorial] — by Wikiomics.org | *[http://wikiomics.org/wiki/Bioinfo_tutorial Bioinfo tutorial] — by Wikiomics.org | ||
| + | *[http://www.inf.fu-berlin.de/inst/ag-bio/FILES/ROOT/Projects/Algorithms/lisa/index.php LiSA] — a software platform for structural alignment algorithms. (including: "T-Lara: RNA multiple Structural Alignment") | ||
| + | *[http://biwww2.informatik.uni-freiburg.de/Software/MARNA/index.html MARNA] — a server for '''M'''ultiple '''A'''lignment of '''RNA'''s. | ||
| + | *[http://pbil.univ-lyon1.fr/software/seaview.html SeaView] — a graphical multiple sequence alignment editor. Able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment. | ||
| + | *[http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=MCOFFEE::Advanced M-Coffee] — computes a multiple sequence alignment and the associated phylogenetic tree by combining the output of several multiple sequence alignment packages (PCMA, Poa, Mafft, Muscle, T-Coffee, ClustalW, ProbCons, DialignT). | ||
| + | |||
| + | ==References== | ||
| + | *O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C (2004). "[http://www.tcoffee.org/Publications/Pdf/3DCoffee.pdf 3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments][[Image:Icon_pdf.gif|PDF]]". ''J Mol Biol, 340:385-395''. | ||
| + | *Notredame C, Higgins D, Heringa J (2000). "[http://www.tcoffee.org/Publications/Pdf/tcoffee.pdf T-Coffee: A novel method for multiple sequence alignments][[Image:Icon_pdf.gif|PDF]]". ''J Mol Biol, 302:205-217''. | ||
| + | *Notredame C, Holme L, Higgins DG (1998). "[http://www.tcoffee.org/Publications/Ps_pdf/coffee.pdf COFFEE: A New Objective Function For Multiple Sequence Alignmnent][[Image:Icon_pdf.gif|PDF]]". ''Bioinformatics, 14(5):407-422''. | ||
| + | *Notredame C, Abergel C (2003). "[http://www.tcoffee.org/Publications/Pdf/core.pp.pdf Using Multiple Alignment Methods to Assess the Quality of Genomic Data Analysis][[Image:Icon_pdf.gif|PDF]]", in ''Bioinformatics and Genomes: Current Perspectives'', M. Andrade, Editor., Horizon Scientific Press. p.30-50. (details on the colour scheme) | ||
==External links== | ==External links== | ||
| Line 20: | Line 30: | ||
*[http://www.tcoffee.org/Documentation/t_coffee/t_coffee_tutorial.htm T-Coffee tutorial] | *[http://www.tcoffee.org/Documentation/t_coffee/t_coffee_tutorial.htm T-Coffee tutorial] | ||
*[http://tcoffee.vital-it.ch/Doc/doc3.html Format documentation] | *[http://tcoffee.vital-it.ch/Doc/doc3.html Format documentation] | ||
| + | *[http://www.tcoffee.org/Documentation/t_coffee/t_coffee_technical.htm Technical notes] | ||
[[Category:Bioinformatics]] | [[Category:Bioinformatics]] | ||
Revision as of 08:13, 20 April 2007
T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity of identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF and FASTA format. The input files are always in FASTA format. Note that what T-Coffee terms "Clustal" format is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX can import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export.
Usage
t_coffee foo.fa
the default output is foo.aln.
Residue types
- charged: KRDE
- polar: NQST
- aliphatic: ILMV
- aromatic: FYW
- others: APCGH
See also
- Clustal
- Bioinfo tutorial — by Wikiomics.org
- LiSA — a software platform for structural alignment algorithms. (including: "T-Lara: RNA multiple Structural Alignment")
- MARNA — a server for Multiple Alignment of RNAs.
- SeaView — a graphical multiple sequence alignment editor. Able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment.
- M-Coffee — computes a multiple sequence alignment and the associated phylogenetic tree by combining the output of several multiple sequence alignment packages (PCMA, Poa, Mafft, Muscle, T-Coffee, ClustalW, ProbCons, DialignT).
References
- O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C (2004). "3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments
". J Mol Biol, 340:385-395. - Notredame C, Higgins D, Heringa J (2000). "T-Coffee: A novel method for multiple sequence alignments". J Mol Biol, 302:205-217.
- Notredame C, Holme L, Higgins DG (1998). "COFFEE: A New Objective Function For Multiple Sequence Alignmnent". Bioinformatics, 14(5):407-422.
- Notredame C, Abergel C (2003). "Using Multiple Alignment Methods to Assess the Quality of Genomic Data Analysis", in Bioinformatics and Genomes: Current Perspectives, M. Andrade, Editor., Horizon Scientific Press. p.30-50. (details on the colour scheme)
External links
- T-Coffee Home Page and Server — include a stand-alone version for download.
- T-Coffee tutorial
- Format documentation
- Technical notes
