[Bioperl-l] graphing trees

Guillaume Rousse rousse at ccr.jussieu.fr
Fri Nov 5 08:50:51 EST 2004

Sean Davis wrote:
> On Nov 5, 2004, at 7:53 AM, Guillaume Rousse wrote:
>> 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 issues.
> Have you thought using R for the calculations/display?  If you have that 
> much data, it might be worthwhile working with it in a computation 
> environment.
Is R usable from a perl program, and not in interactive way only ? And 
this would only be a replacement for Algorithm-Cluster, which works 
quite well (it is a wrapper around a C library), that wouldn't get me 
rid of the task of building the Bio::Tree Object manually. I was just 
asking if a clustering algorithm was available from bioperl itself.

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