[Bioperl-l] Displaying an alignment using Bio::Graphics

Lincoln Stein lstein at cshl.edu
Mon Aug 23 12:31:28 EDT 2004

There's a colorized multiple alignment display in the GBrowse package 
(http://www.mod.org).  It's in the module 

There's also a very handy module called Bio::Graphics::Browser::Markup 
that can be used to add HTML text style strings (colors, boldface, 
italics and various combinations) to arbitrary DNA and protein 
sequences.  It takes care of all the line-wrapping and collisions 
among the tags.  You just need to provide the base pair range and a 
symbolic style name.


On Tuesday 10 August 2004 07:52 am, Iain Wallace wrote:
> Hi all,
> I was wondering if any one knows how to display a multiple sequence
> alignment using the Bio::Graphics modules.
> Ideally I would like to colour in certain columns depending on a
> mask that I have created ?
> (FYI The particular project is to colour in the columns of a test
> alignment which have corresponing columns in a reference
> alignment).
> thanks
> Iain Wallace
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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