colorizing multiple alignments

Harry see at sig.for.address
Fri Oct 1 19:58:55 EST 1999

In article <m3puz0xfi3.fsf at>, john s jacobs
anderson <jacobs at> wrote:

> I have some multiple sequence alignments that I would like to colorize
> on the basis of amino acid identity and similarity. Are there any
> *nix, MacOS, or web-based tools that people would recommend for this?

I recommend Boxshade- the Unix version is very serviceable but if you have
access to a Mac, the Mac version (called appropriately enough MacBoxshade)
really simplifies the interface. There's also a web-based interface.

The link I have for Boxshade is down right now:


but you can pull the Mac version from here:



Harry <h3 at>

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