WSMuscle Clients


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

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:

Web Service

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

C# .NET Client

.NET runtime

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

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

Get the client

Download the C# client:

Run without arguments to get a usage summary:


Java Client


Download and unzip the library files and add the jars to the Java classpath.

Get the client

Download the Java client:

To get usage information run the client without arguments:

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

Perl Client

Install SOAP::Lite

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.

Get the client

Then download the Perl client:

To get usage information run the client with no arguments:



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.

services/archive/msa/wsmuscle_clients.txt · Last modified: 2013/04/23 16:29 by hpm