[BioPython] Cladograms

[Giovanni Marco Dall'Olio]

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?

> 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?

>
> 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
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