[Bioperl-l] Bio::Tree development

Lucia Peixoto luciap at sas.upenn.edu
Fri Jan 19 20:53:11 UTC 2007


One of the functions missing from TreeIO that will be good to implement is a
collpase bootstrap function, meaning to collapse all nodes bellow a certain
bootstrap value

I do have a bit of code to do this, however it cannot be generalized until the
bootstrap value is consistently captured by the same function, so far, for the
trees I have at least, the internal ID is the bootstrap value, but that may not
be true for all trees.Or it can be written asuming that you already set the
boostrap to the right value.

The function bootstrap in Bio::Tree::NodeI never gets the bootstrap right in any
tree I've used (always newick format I am talking)

just an idea,


Quoting Chris Fields <cjfields at uiuc.edu>:

> On Jan 19, 2007, at 1:18 PM, Sendu Bala wrote:
> ...
> >
> >> * General code cleanup
> >> Making sure everything is indented according to some standard. I've
> >> seen previously that there doesn't seem to be any real standard for
> >> how BioPerl code should look like. I would think that it would be a
> >> lot clearer to understand lots of the code if it was indented
> >> properly. As it is now, the indentation depth changes between 2,3 and
> >> 4 within the same file even.
> >
> > My own personal preference is an indent of 4 spaces.
> ...
> Mine as well.  Some people also use tabs vs spaces (I prefer
> spaces).  However, I think (Johan) you'll be hard-pressed to force a
> standard there.
> You're always welcome to run it through perltidy prior to commits!
> chris
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Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania

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