[Bioclusters] paup output parsing

[Jason Stajich]

In Bioperl, the module Bio::TreeIO::nexus will parse PAUP trees.

You may have to grab the latest version of this module from CVS in order
to get all the fixes since the 1.4.0 release.  I can't remember when all
the changes were checked in.

-jason
On Thu, 8 Apr 2004, Ognen Duzlevski wrote:

> Hi all,
>
> I am trying to parse out paup output such as this one:
> tree PAUP_1 = [&U] (1:4,2:20,((3:14,5:200):17,4:13):24);
>
> What I want is to extract the length for each one. The number after : is
> the length
>
> For this case:
> Length of 1 will be 4
> Length of 2 will be 20
> Length of 3 will be 14+17+24=55
> Length of 5 will be 200+17+24=241
> Length of 4 will be 13+24=3
>
> Naturally, the output gets pretty large and complicated and before I fire
> up my editor and start coding: are there any tools/scripts outhere that
> extract this information already and are available for download?
>
> Thanks,
> Ognen
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu