T-coffee - Revision history

Rf at 17:57, 24 November 2016

2016-11-24T17:57:40Z

Rf at 17:45, 24 November 2016

2016-11-24T17:45:30Z

Rf at 17:26, 24 November 2016

2016-11-24T17:26:31Z

Rf: Created page with "= Introduction = Multiple sequence aligner ... especially proteins, Cedric Notredame of the CRG in Barcelona. It's quite large program with many options and is capable of in..."

2016-11-24T17:15:09Z

Created page with "= Introduction = Multiple sequence aligner ... especially proteins, Cedric Notredame of the CRG in Barcelona. It's quite large program with many options and is capable of in..."

New page

= Introduction =

Multiple sequence aligner ... especially proteins, Cedric Notredame of the CRG in Barcelona.

It's quite large program with many options and is capable of interaction with a number of other aligners, especially Clustal as Cedric has often collaborated with Desmond Higgins.

= Usage =

T-coffee is a predominantly command-line program. If you want proteins alignments using a Graphical User Interface, try clustalx.

Despite the dash in its name, the T-coffee executable is actually '''t_coffee''' with an underscore.

As input it can take various types of data such as

* '''P''' : PDB structure
* '''S''' : Sequences (aligned or unaligned sequences)
* '''M''' : Methods used to build the library
* '''L''' : Precomputed T-Coffee library
* '''A''' : Alignments that must be turned into a Library
* '''X''' : Substitution matrices
* '''R''' : Profiles

The letter can be used with tjhe '''-in''' option. Alternative options such as '''-seq''' also exist so that feedign the program an unaligned, multifasta file is as easy as:
t_coffee -seq sh3.fasta

← Older revision		Revision as of 17:57, 24 November 2016
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	These letters can be used with the '''-in''' option. Alternative options such as '''-seq''' also exist so that feedign the program an unaligned, multifasta file is as easy as:		These letters can be used with the '''-in''' option. Alternative options such as '''-seq''' also exist so that feedign the program an unaligned, multifasta file is as easy as:
−	t_coffee -seq sh3.fasta	+	t_coffee -seq sh3.fasta -outfile <yourchoiceofname.aln>
		+
		+	In this case the result will be output to a file called "yourchoiceofname.aln" which will be in clustal format. It will also output a file called "youchoiceofname.aln.html" which is a colorized, more visually friendly version of the alignment whihc can be viewed in a browser.

← Older revision		Revision as of 17:45, 24 November 2016
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	It's quite large program with many options and is capable of interaction with a number of other aligners, especially Clustal as Cedric has often collaborated with Desmond Higgins.		It's quite large program with many options and is capable of interaction with a number of other aligners, especially Clustal as Cedric has often collaborated with Desmond Higgins.
		+
		+	T-Coffee stands for "Tree based Consistency Objective Function For alignment Evaluation". Its main distinction is that of being a consistency based aligner.
		+

	= Usage =		= Usage =

@@ Line 21: / Line 21: @@
 * '''R''' : Profiles
-The letter can be used with tjhe '''-in''' option. Alternative options such as '''-seq''' also exist so that feedign the program an unaligned, multifasta file is as easy as:
+These letters can be used with the '''-in''' option. Alternative options such as '''-seq''' also exist so that feedign the program an unaligned, multifasta file is as easy as:
   t_coffee -seq sh3.fasta