JalView - Java alignment editor

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Jalview -

a - multiple alignment editor

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Downloads

Jalview

- Examples

Applet
Application

- Reference

"The Jalview Java
- Alignment Editor,"
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Bioinformatics, 12, 426-7

- Source Code

Jalview 2

Feedback

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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.
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Version 2.0 is the latest release - version of Jalview. This version has many new features compared to the - original version.

The original version of Jalview, version - 1.18, can still be downloaded. Some features no longer work.

- Jalview Features -- See major new developments by trying Jalview - Version 2 --

Sequence feature retrieval and display on the alignment
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
Alignment sorting options (by name, tree order, percent identity, - group)
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
EPS, PNG files can be generated for inclusion in documents

- Authors :
- Version 1.18 Michele Clamp; James Cuff; Stephen Searle; Geoff Barton
- V ersion 2.0 Andrew Waterhouse; Jim Procter; Geoff Barton -

Special thanks go to Alex Bateman and the Pfam team for using Jalview - and making many helpful suggestions

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.

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