It sounds like you would like a module that will read the HTML file, render it, and then write out a png or jpeg image of the rendered page. Perhaps someone else knows of such a beast, but my cursory look through CPAN did not turn this up.

Since the structure of the figure is relatively simple, a bunch of tables each containing rectangle-on-a-line with varying offsets, you may be better off parsing the HTML file to extract the sequence information and offset data (the first "td width=" in each table) and rendering rectangle-on-a-lines in PNG using GD::Simple. This would give you more control over the appearance of the image

Update:Ooh, Look at that! Corion found a module that would work after all.