Jalview - a java multiple alignment editor

(1.3 beta release 23rd September 1998)

(1.6.4b and 1.7b available 23rd December 1998)


Try jalview

Download 1.3b/1.0b
(1.6.4b and 1.7 available)

HTML parameter example


align and/or view your own sequences

 Jalview documentation


19th November 1998 - mail output from jalview should now be fixed

Jalview is being used in:

 (Note: Netscape4.05, IE4 or HotJava1.1 are needed. Older browsers give no or unsatisfactory results.)

Introduction and features

Jalview is a multiple alignment editor written entirely in java.  It was initially to be used as a visualization tool for the Pfam CORBA server and client at the EBI but is available as a general purpose alignment editor.
  New in 1.3b

 New in 1.2b

Jalview's other features include: Why write a multiple alignment editor?  There are certainly good programs out there (e.g. seaview and Cinema and a very special mention for belvu even though it's not an editor) but none of them have all the features I want.   I wanted to combine display speed and consensus colour schemes  with easy access to the databases available on the internet using CORBA or CGI.

The ability to run java applets in web browsers is probably the most important reason for using java as it enables the software to be easily accessed from almost anywhere and easy integration with sequence databases available on the web.  The speed of the java VMs is improving and much helped by just-in-time compilers although java can not claim to be winning any points for speed of execution.

Further information available from  M.Clamp
Last update 10th June 1998