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

• MUSCLE (REST)
• MUSCLE (SOAP)

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

MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW or T-Coffee, depending on the chosen options. Multiple alignments of protein sequences are important in many applications, including phylogenetic tree estimation, secondary structure prediction and critical residue identification.

For more information about this tool see:

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

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

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: wsmuscle.exe
• Source code: wsmuscle.cs

Run without arguments to get a usage summary:

wsmuscle.exe

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

Download the Java client:

• Executable: WSMuscle.jar
• Source code: WSMuscleClient.java

To get usage information run the client without arguments:

java -Djava.ext.dirs=lib -jar WSMuscle.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. You can get version 0.60 from CPAN.

Then download the Perl client: muscle.pl

To get usage information run the client with no arguments:

perl muscle.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 WSMuscle can be found on myExperiment.