T-Coffee - Revision history

Christoph at 03:25, 22 September 2008

2008-09-22T03:25:53Z

Christoph: /* See also */

2007-07-30T07:18:54Z

‎See also

Christoph at 08:13, 20 April 2007

2007-04-20T08:13:45Z

Christoph: /* External links */

2007-04-20T07:52:34Z

‎External links

Christoph: /* External links */

2007-04-20T07:50:56Z

‎External links

Christoph at 07:49, 20 April 2007

2007-04-20T07:49:58Z

Christoph: /* See also */

2007-02-10T02:49:16Z

‎See also

Christoph at 02:47, 10 February 2007

2007-02-10T02:47:33Z

New page

'''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 [[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==
t_coffee foo.fa
the default output is <code>foo.aln</code>.

==See also==
*[[Clustal]]

==External links==
*[http://www.tcoffee.org T-Coffee Home Page and Server] — include a stand-alone version for download.

[[Category:Bioinformatics]]

@@ Line 1: / Line 1: @@
 '''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==
   t_coffee foo.fa
-the default output is <code>foo.aln</code>.
+the default output is:
 ==Residue types==

@@ Line 14: / Line 14: @@
 ==See also==
 *[[Clustal]]
 *[http://wikiomics.org/wiki/Bioinfo_tutorial Bioinfo tutorial] &mdash; by Wikiomics.org
 *[http://www.inf.fu-berlin.de/inst/ag-bio/FILES/ROOT/Projects/Algorithms/lisa/index.php LiSA] &mdash; 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] &mdash; a server for '''M'''ultiple '''A'''lignment of '''RNA'''s.
 *[http://pbil.univ-lyon1.fr/software/seaview.html SeaView] &mdash; 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] &mdash; 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==

@@ Line 1: / Line 1: @@
-'''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 [[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.
+'''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==
@@ Line 15: / Line 15: @@
 *[[Clustal]]
 *[http://wikiomics.org/wiki/Bioinfo_tutorial Bioinfo tutorial] &mdash; by Wikiomics.org
 ==External links==
@@ Line 20: / Line 30: @@
 *[http://www.tcoffee.org/Documentation/t_coffee/t_coffee_tutorial.htm T-Coffee tutorial]
 *[http://tcoffee.vital-it.ch/Doc/doc3.html Format documentation]
 [[Category:Bioinformatics]]

@@ Line 18: / Line 18: @@
 ==External links==
 *[http://www.tcoffee.org T-Coffee Home Page and Server] &mdash; include a stand-alone version for download.
 *[http://tcoffee.vital-it.ch/Doc/doc3.html Format documentation]
 [[Category:Bioinformatics]]