[Biojava-dev] some code I've knocked up

[Lachlan James Coin]

Matthew,

Do you know about the phylogenetic analysis library 
(see http://www.stat.uni-muenchen.de/~strimmer/pal-project/)
This is a full phylogenetics package written in Java.  I have also been doing 
some tree stuff and hence have been using this package.  It has a lot of the 
tree manipulation stuff in it already.  Also there is a package called 
forrester, written by Christian Zmasek, one of Sean Eddy's students which also 
manipulates trees.  One of the nicest things about this package is the ATV 
tree viewer applet.  

It would be nice to incorporate these packages into biojava - at the moment 
for instance you need to convert between a biojava alignment and a pal 
alignment for instance (which isn't that hard, but still).

Cheers,

Lachlan



Quoting Matthew Pocock <matthew_pocock at yahoo.co.uk>:

> Hi,
> 
> For my sins (which I guess must be many and varied), I've been working 
> with some expression data the last week. There isn't anything in biojava 
> that helps out here. I had to write code to parse files with tables 
> (e.g. tab delimited text files) and to manipulate trees.
> 
> The javadoc (undocumented) is up at http://www-ihg.ncl.ac.uk/mopo
> 
> I'd apreciate any comments anyone has about it. I think Table needs to 
> be extended to include both row and column titles. Some of the method 
> names suck. The cluster algorithms need testing on some 3rd party data 
> to make sure they do what they are meant to do.
> 
> Perhaps after a good dusting down, some of this could make its way into 
> biojava.
> 
> Matthew
> 
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