[Bioperl-l] Draw phylogenetic trees with bar chart

K. Shameer shameer at ncbs.res.in
Wed Nov 12 03:16:35 EST 2008

Hi Florent,

I recently used the Bio::Tree::Draw::Cladogram method to generate trees
using input files in newick format. I used the eps format output and used
the `convert` (part of ImageMagick) tool to convert it in to png format.
The example in the HOWTO worked quite well for me. I am not sure if you
can add graph data as bar chart using BioPerl.

K. Shameer

> Dear Bioperl users,
> I need to represent graphically phylogenetic trees as cladograms or
> phylograms using Perl. An additional requirement is that I would like to
> add graph data as bar chart on top of it as in this example:
>     http://scums.sdsu.edu/Mapper/images/b.gif
> Now, I have read the BioPerl howto and know about the
> Bio::TreeIO::svggraph and Bio::Tree::Draw::Cladogram modules. The first
> one uses the SVG Perl module whereas the other one uses the PostScript
> module to create EPS images. I do not know why there are 2 very similar
> modules to draw trees (in different locations), but none of them seem to
> able to plot additional information on the tree.
> Is there any other Perl code that you know of that would facilitate
> doing what I want to do? If not, how should I modify one of the 2
> mentioned BioPerl modules to plot bar charts, and which one??
> Thanks,
> Florent
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