Jalview - a java multiple alignment editor
(1.3 beta release 23rd September 1998)
(1.6.4b and 1.7b available 23rd December 1998)
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
- Sequence feature retrieval and display on the alignment using SRS
- Conservation analysis similar to that of AMAS
- Group editing (insertion deletion of gaps in groups of sequences).
- Removal of gapped columns
- Extra colour schemes (secondary structure propensities mostly)
- Saving postscript and text to local files (application only)
- Extra sorting options (by tree order, by group)
- A mini browser for displaying SRS output for applications.
- Linking of group colours between the alignment, tree and PCA windows.
- Extra command line options to set the SRS server and database
New in 1.2b
Jalview's other features include:
User definable colour schemes.
Taylor colour scheme added
UPGMA and NJ trees calculated and drawn based on percent identity
Sequence clustering using principal component analysis.
Extra fonts and 2 drawing modes.
Removal of redundant sequences.
Aligns sequences using local clustalw (application
only) or remotely at the EBI
*** New in 1.1b version ***
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.
Variable font sizes/colours
Colour by amino acid physico-chemical property,
similarity to consensus sequence, hydrophobicity or secondary structure.
Sequences can be grouped and coloured differently.
Smith Waterman pairwise alignment of selected
Sort sequences by pairwise identity to
consensus or selected sequence.
Consensus sequence calculations
Removal of redundant sequences (coming
Gaps can be inserted/deleted using the
Input from URL/local file (if running as
application ) or cut and paste in textbox
Common formats supported - msf,fasta, clustal,
Text output via email/browser.
Links to swissprot SRS server at EBI.
Colour postscript output via email.
HTML parameters let you input sequences
and groups and colour schemes.
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