2004: Jalview paper published: Clamp, M., Cuff, J., Searle, S. M. and
Barton, G. J. (2004), "The Jalview Java Alignment Editor", Bioinformatics, 12, 426-7. [PubMed][PDF]
Please cite this paper if you use Jalview in your work. Thank you.
23rd November 2004
New Jalview development has been funded for three years from 1st
October 2004 by the BBSRC
of the "Visualisation and Analysis of Biological Sequences, Alignments
and Structures" Project. This project is coordinated by Geoff
Barton at the University of
with partners at EBI and BioSS and consultancy (blessing :-) from
Michele Clamp; the originator of Jalview. More details of
this funding and the new developments will be posted here
Introduction and features
Jalview is a multiple alignment editor written in java. It is used widely in a
variety of web pages (e.g. the EBI clustalw server and the PFAM protein
database) but is available as a general purpose alignment editor.
retrieval and display on the alignment using SRS
Reads and writes
alignments in a variety of formats
Gaps can be
inserted/deleted using the mouse.
analysis similar to that of AMAS
(insertion deletion of gaps in groups of sequences).
Removal of gapped
and text to local files (application only)
options (by name, tree order, percent identity, group)
A mini browser for
displaying SRS output for applications.
Linking of group
colours between the alignment, tree and PCA windows.
NJ trees calculated and drawn based on percent identity distances.
clustering using principal component analysis
pairwise alignment of selected sequences