[BioPython] Cladograms

[Renato Alves]

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(). Also 
google doesn't give the best results when searching for R <something>.
Still I would like to remain in python as much as possible. I used rpy 
before to do some R from within python and it worked but the code is far 
from "maintainable".
>> but where the trees will be
>> cladograms[2] instead of the result of clustering steps.
>> I know that probably I won't find modules doing exactly what I want, which
>> is why I'm searching for tools to do each step separately and try to glue
>> them somehow. For the heatmap I have something already that will probably do
>> the job, but for the cladograms I couldn't find any decent module.
>> Do you happen to know any dark alley in BioPython or any other external
>> module that would allow me to do the cladogram?
>>     
> But from which kind of data?
> Do you have to align sequences, or are they aligned already? do you
> already have the cladograms, or do you have to calculate them?
>   
The data will be mostly taxonomic and in some cases genes grouped by 
properties. I only need to find a simple way to turn it into an image.

Thanks
>> Thanks,
>> Renato
>>
>> [1] -
>> http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/heatmap/default_heatmap.png
>> [2] -
>> http://www.csupomona.edu/~jcclark/classes/bot125/resource/graphics/c/cladogram.gif
>> _______________________________________________
>> BioPython mailing list  -  BioPython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>