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

• MAFFT (REST)
• MAFFT (SOAP)

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

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.

For more information about this tool see:

• EMBL-EBI Tools:
  • MAFFT
  • MAFFT Help
• MAFFT website

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

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: wsmafft.exe
• Source code: wsmafft.cs

Run without arguments to get a usage summary:

wsmafft.exe

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

Download the Java client:

• Executable: WSMafft.jar
• Source code: WSMafftClient.java

To get usage information run the client without arguments:

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

To run the Perl client you should install SOAP::Lite first. SOAP::Lite is a collection of Perl modules which provides a simple and lightweight interface to the Simple Object Access Protocol (SOAP) both on client and server side. The client requires SOAP::Lite version 0.60.

Download the Perl client: mafft.pl

To get usage information run:

perl mafft.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 WSMafft can be found on myExperiment.