[Biojava-l] Parsing Code for Phylogenetic Trees

Matthew Pocock mrp@sanger.ac.uk
Thu, 08 Mar 2001 11:18:27 +0000

ozborn@UVic.CA wrote:

> Does anybody have any parsing code for phylogenetic trees?  I am looking
> for something that will take in either .ph or .nj format.  I want to
> construct a species trees from gene trees, any data structure that it gets
> parsed into will be fine I'm sure.

If you download the source-code release of my expression browser 
  link browser-src.jar), you will find the source-code for a tree 
parser. I didn't write the code, and your milage may vary.

> I also ported the Perl code for calculation of isoelectric point to Java
> if anybody wants it.  I don't know how to contribute it to biojava quite
> yet.

This would be great to have. We already have a proteomics package, so 
mabey it naturaly lives there. If you are interested in contributing the 
code, then please contact me personaly and we can work out accounts etc. 
and quickly discuss ways to BioJava'ise the code.

All the best,


>  -John
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