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Pretty Printing and Shading of Multiple-Alignment files

You can also download pyBoxshade, a desktop application for colouring/shading sequence alignments: https://github.com/mdbaron42/pyBoxshade

This server uses version 3.21 of BOXSHADE, written by K. Hofmann and M. Baron. BOXSHADE is in the public domain and available from Source Forge http://sourceforge.net/projects/boxshade/

This server takes a multiple-alignment file in either GCG's MSF-format or Clustal ALN-format.
Output can be created in the following formats:

  • Postscript/EPS (using shaded background)

  • RTF old (using colors)

  • RTF new (using shaded background)

  • XFIG-files (using shaded background)

  • ASCII (showing similarities)

  • ASCII (showing differences)

  • HPGL (using colors)

  • PICT (for later editing on MACs and PCs)

If you have problems using this server (like getting no result), read this and see the FAQ list.

Output format

Font Size

Consensus Line

Fraction of sequences:

Enter sequence number:

(that must agree for shading)

only if 'consensus to a single sequence' is required

Query title (optional)

  • When pasting MSF or ClustalW files, please make sure
    that the pasted text starts with the header line of the alignment and
    contains no extra blank lines at the bottom.

Input sequence format

Paste your multiple-alignment file
(see above for valid formats)