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Jalview Description

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.

Use Jalview for:

* Viewing
o Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)
o Save alignments and associated trees in Jalview XML format.

* Editing
o Gaps can be inserted/deleted using the mouse or keyboard.
o Group editing (insertion deletion of gaps in groups of sequences).
o Removal of gapped columns.

* Analysis
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.

* Annotation
o Use 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.

* Publishing
o Print your alignment with colours and annotations.
o Create HTML pages.
o Output alignment as portable network graphics image (PNG).
o Output alignment as encapsulated postscript file (EPS).

Jalview Version History

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Jalview User Reviews

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