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
as part
of the "Visualisation and Analysis of Biological Sequences, Alignments
and Structures" Project. This project is coordinated by Geoff
Barton at the University of
Dundee
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
shortly.
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
domain
database) but is available as a general purpose alignment editor.
Features
Sequence feature
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.
Conservation
analysis similar to that of AMAS
Group editing
(insertion deletion of gaps in groups of sequences).
Removal of gapped
columns
Many different
colour schemes
Saving postscript
and text to local files (application only)
Alignment sorting
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.
UPGMA and
NJ trees calculated and drawn based on percent identity distances.
Sequence
clustering using principal component analysis
Removal of
redundant sequences
Smith Waterman
pairwise alignment of selected sequences
