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