On Monday 28th March 2011 the WSTCoffee service, used by these clients, was decommissioned and replaced by the following services:

• T-COFFEE (REST)
• T-COFFEE (SOAP)

The service documentation and clients below are historical and provided solely for reference purposes.

T-Coffee is a multiple sequence alignment program. Multiple sequence alignment programs are meant to align a set of sequences previously gathered using other programs such as BLAST or FASTA. The main characteristic of T-Coffee is that it will allow you to combine results obtained with several alignment methods. For instance if you have an alignment coming from ClustalW, an other alignment coming from Dialign, and a structural alignment of some of your sequences, T-Coffee will combine all that information and produce a new multiple sequence having the best agreement with all these methods. By default, T-Coffee will compare all your sequences two by two, producing a global alignment and a series of local alignments (using lalign). The program will then combine all these alignments into a multiple alignment.

For more information about this tool see:

• EBI Tools:
  • T-Coffee
  • T-Coffee Help
• T-Coffee website

For details of the service used by these clients see WSTCoffee.

The Microsoft .NET runtime is already installed on most MS Windows systems. The Microsoft .NET runtime is available via Microsoft Update or as a download (see http://msdn.microsoft.com/netframework/).

For MacOS X, Linux and other non-Windows systems see Mono or DotGNU.

Download the C# client:

• Executable: wstcoffee.exe
• Source code: wstcoffee.cs

Run without arguments to get a usage summary:

wstcoffee.exe

Download and unzip the library files lib-1.4.zip and add the jars to the Java classpath.

Download the Java client:

• Executable: WSTCoffee.jar
• Source code: WSTCoffeeClient.java

To get usage information run the client without arguments:

java -Djava.ext.dirs=lib -jar WSTCoffee.jar

To run the Perl client you need to install SOAP::Lite. SOAP::Lite is a collection of Perl modules which provides a simple and lightweight interface to the Simple Object Access Protocol (SOAP) for both client and server applications. This client requires SOAP::Lite version 0.60.

Download the Perl client: tcoffee.pl

To get usage information run the script without arguments:

perl tcoffee.pl

Workflow engines such as Taverna and Triana offer a simple way of combining individual web services into complex applications.

A basic workflow showing how to use WSTCoffee can be found on myExperiment.