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

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


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence*
  • Computer Graphics
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Publishing / standards
  • Sequence Alignment / methods*
  • Software*
  • User-Computer Interface


  • Proteins