[Bioperl-l] Bio::TreeIO

Ardell, David dave.ardell@ebc.uu.se
Sat, 02 Feb 2002 00:58:05 +0100 (CET)

Dear Bioperl colleagues

I have been planning to introduce myself for about a month,
right before I started traveling in the states from sweden. I have been
using bioperl 0.7.0 for about a year and have written scripts
and modified modules for my own use.

First, I want to say thanks for your efforts. bioperl is great
and just about essentially useful for what I do (I have a population genetics 
background and am currently doing microbial genomics and molecular evolution)..
it has saved my skin in several accounts.

Secondly, I have suggestions and scripts to contribute but have been 
bashful about sending something off to you because I am not caught up
with the state of your development efforts.

Lastly, I am writing now anyway because I saw something about a Bio::TreeIO 
mentioned on your list. I have developed Tree and TreeIO modules. I'd 
like to propose integrating them into bioperl, so long as i haven't reduplicated 
any of your efforts. 

The state of the modules is that they are currently suited for representing 
trees and tree formats, but are agnostic as to what kind of objects are at the 
tips of the trees. They are not explicitly bioperl and do not inherit the 
bioperl root object or interface.

I am writing up a short publication about the modules as they are ready to be 
used by others (minus some documentation) and I want them to find a good home. 

I think what I would like to do is package them free-standing for the 
phylogenetics community to use. But, so long as you don't already have something 
like this in the pipeline, I would be open to contributing them to your project,  
and be interested in helping to plan how they could be integrated nicely inside 
bioperl with the alignment, sequence, and taxon representations. I would also be 
interested in writing modules to drive phylogenetics software and eat their 

Good luck with the new release!

perl on