[Bioperl-l] graphing trees

Guillaume Rousse rousse at ccr.jussieu.fr
Fri Nov 5 07:53:35 EST 2004

Jason Stajich wrote:
> 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.
Seems the most interesting right now.

Actually, I currently build my tree by first computing a distance matrix 
from my raw data, passing it to the Algorithm-Cluster module, and 
building nodes from its ouput. So the most logical way would be to 
implement a new Bio::TreeIO::cluster module, constructing a Bio::Tree 
object from this output, and using Bio::TreeIO::svggraph to output my 
graph. Would such piece of code eventually interest bioperl maintainers ?

Alternatively, if there was a way to construct the nodes list from the 
matrix distance directly in BioPerl, so as to bypass Algorithm-Cluster, 
I could also get interested. I am just effraid that with a 3000 x 3000 
matrix, a pure-perl implementation of the clustering could have perfs 

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