[BioPython] Cladograms

[David Winter]

Renato Alves wrote:
> Quoting Giovanni Marco Dall'Olio on 11/27/2008 04:45 PM:
>> On Thu, Nov 27, 2008 at 4:17 PM, Renato Alves 
>> <rjalves at igc.gulbenkian.pt> wrote:
>>  
>>> Hi everyone,
>>>
>>> I've been searching the web for python modules to do cladograms but 
>>> the only
>>> relevant stuff I found was relative to dendograms and hierarchical
>>> clustering which will give the representation I need.
>>> My goal is something that resembles a heatmap[1]
>>>     
>> Let me premise that I am not able to help you :).
>> But this seems to be the kind of things that R does. Have you had a 
>> look at it?
>>   
> For the heatmap I did have a look and seems easy to use, for the 
> cladograms I couldn't find much using the name with help.search(). 
[snip]

Hi renato,

Have you looked into the R package  ape (analysis of phylogentics and 
evolution, install.packages("ape")) - it has object classes for phylip 
and nexus trees. I don't know how easy it is to kludge things together 
from different packages but it might be worth looking into? There is a 
python module to integrate with R if you want to stay pure ;)

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