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Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):510-2. doi: 10.1107/S0907444909007835. Epub 2009 Apr 18.

ALINE: a WYSIWYG protein-sequence alignment editor for publication-quality alignments.

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School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.


Marked-up sequence alignments typically provide the central figure in articles describing proteins, whether in the fields of biochemistry, bioinformatics or structural biology. The generation of these figures is often unwieldy: interactive programs are often aesthetically limited and the use of batch programs requires the repetitive iterative editing of scripts. ALINE is a portable interactive graphical sequence-alignment editor implemented in Perl/Tk which produces publication-quality sequence-alignment figures where "what you see is what you get". ALINE is freely available for download from

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