Difference between revisions of "T-coffee"
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* '''R''' : Profiles | * '''R''' : Profiles | ||
| − | + | 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 | ||
Revision as of 17:26, 24 November 2016
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
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
