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) and is also available as a general purpose alignment editor.

o Reads and writes alignments in a variety of formats
o Gaps can be inserted/deleted using the mouse.
o Group editing (insertion deletion of gaps in groups of sequences).
o Removal of gapped columns.
o Align sequences using Web Services (Clustal, Muscle...)
o Amino acid conservation analysis similar to that of AMAS.
o Alignment sorting options (by name, tree order, percent identity, group).
o UPGMA and NJ trees calculated and drawn based on percent identity distances.
o Sequence clustering using principal component analysis.
o Removal of redundant sequences.
o Smith Waterman pairwise alignment of selected sequences.
o Web based secondary structure prediction programs (JNet).
o User predefined or custom colour schemes to colour alignments or groups.
o Sequence feature retrieval and display on the alignment.
o Print your alignment with colours and annotations.
o Output alignments as HTML pages, images (PNG) or postscript (EPS).

If you use Jalview in your work, please quote this publication. Clamp, M., et
al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7

WWW: http://www.jalview.org