WSKalign Clients


On Monday 28th March 2011 the WSKalign 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.


A fast and accurate multiple sequence alignment algorithm.

For more information about this tool see:

Web Service

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

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 WSKalign.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. The client requires SOAP::Lite version 0.60.

Get the client

Download the Perl client:

To get details of usage run:



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 WSKalign can be found on myExperiment.

services/archive/msa/wskalign_clients.txt · Last modified: 2013/04/23 16:28 by hpm