[Bioperl-l] graphing trees

[Jason Stajich]

On Nov 3, 2004, at 8:39 AM, Guillaume Rousse wrote:

> Hello.
>
> I have large trees to graph, the same way as phylogenetic trees are 
> usually drawn, with edges length expressing distances between nodes.
>
Bio::TreeIO::svggraph generates SVG.

You can also look at the Stoltzfus NEXUS nexplot tool
http://camel5.umbi.umd.edu/camel/software/ which can produce postscript 
versions of trees.

PHYLIP's drawtree and drawgram with the modules 
Bio::Tools::Run::Phylo::Phylip::DrawTree and DrawGram.  This produces 
postscript files.

> I had a quick look at BioPerl HowTos, but there was nothing about 
> visual output in the Phylogenetic Tree HOWTO, and the Bio::Graphics 
> HOWTO says nothing about trees.
>
> So, is there any way to easily draw such kind of visual tree, either 
> in bioperl or outside ?
I assume you are asking about this for programatic soln?

Lots of tree drawing software for tree-at-a-time analysis like 
TreeView, NJPlot, many more.

There is also treeplot (cmdline, can be scripted to produce a lot of 
trees).

-jason

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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/