[BioPython] Cladograms
Renato Alves
rjalves at igc.gulbenkian.pt
Fri Nov 28 11:54:19 UTC 2008
@David and Giovanni
Thank you both for your feedback.
I guess I will give R a more decent try.
In the meanwhile I guess I found myself a python small side project :) .
I will be sure to contribute with the code if I get to any decent result.
Renato
Quoting David Winter on 11/27/2008 09:52 PM:
> 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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