colorizing multiple alignments

[Harry]

In article <m3puz0xfi3.fsf at penguin.biosci.arizona.edu>, john s jacobs
anderson <jacobs at penguin.biosci.arizona.edu> 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:

<http://ulrec3.unil.ch/software/BOX_form.html>

but you can pull the Mac version from here:

<http://maltose.ribs.ucla.edu/macboxshade-2.1.sit.hqx>

-Harry

-- 
Harry <h3 at ucla.edu>