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Jalview is a multiple sequence alignment editor & viewer written in the Java programming language. 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.
Waterhouse A, Procter J, Barton G, Martin D. (University of Dundee) Original Version by Clamp M, Cuff J, Searle S, Barton G
UNIX, Linux, Mac, MS-Windows
Additional recommended knowledge
Use Jalview for:
Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)
Save alignments and associated trees in Jalview XML format.
Gaps can be inserted/deleted using the mouse or keyboard.
Group editing (insertion deletion of gaps in groups of sequences).
Removal of gapped columns.
Align sequences using Web Services (Clustal, Muscle...)
Amino acid conservation analysis similar to that of AMAS.
Alignment sorting options (by name, tree order, percent identity, group).
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.
Use web based secondary structure prediction programs (JNet).
User predefined or custom colour schemes to colour alignments or groups.
Sequence feature retrieval and display on the alignment.
Print your alignment with colours and annotations.
Create HTML pages.
Output alignment as portable network graphics image (PNG).
Output alignment as encapsulated postscript file (EPS).
This article is licensed under the
GNU Free Documentation License. It uses material from the Wikipedia article "Jalview". A list of authors is available in Wikipedia.
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