Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Badges Web report

Making alignments prettier

Mar Albà

Genome Biology 2000, 1:reports2047  doi:10.1186/gb-2000-1-2-reports2047

The electronic version of this article is the complete one and can be found online at:

Received:9 June 2000
Published:19 July 2000

© 2000 BioMed Central Ltd


BoxShade takes sequence alignments in Genetics Computer Group (GCG) PileUp's MSF format or ClustalW's ALN format and creates an output file in which the alignment is displayed with identical or similar residues shaded in two different tones of gray. The proportion of sequences in an alignment that need to have the identical/similar residue before the residue is shaded can be specified by the user; 50% is the default. BoxShade does not generate alignments and is not an editing program. It can, however, be very useful for creating high-quality black-and-white figures for publication. The site contains the latest version of the program, 3.21.


Navigation is very straightforward, with the input form on the opening page, and links to an FAQ page.

Reporter's comments

Best feature

This is a very easy way to shade residues in an alignment. There is a good range of output formats, for example postscript (.EPS, .PDF), rich text (.RTF) (for Word, for example), hypertext (.HGML) and image (.PICT).

Worst feature

Some familiarity with the output format options is needed, as the different formats are not properly documented.

Wish list

Autodetection of alignment format, being able to input alignments from file as an alternative to paste in a window, and more options for color shading would all be desirable.

Related websites

Sites that provide sequence alignment, editing and presentation facilities include PRETTYBOX, ClustalW at the European Bioinformatics Institute, CINEMA, and Jalview.

Table of links

Assumptions made about all sites unless otherwise specified:
The site is free, in English and no registration is required. It is relatively quick to download, can be navigated by an 'intermediate' user, and no problems with connection were found. The site does not stipulate that any particular browser be used and no special software/plug-ins are required to view the site. There are relatively few gratuitous images and each page has its own URL, allowing it to be bookmarked.