I was thinking about incorporating some of the source from Jalview into
biojava. This has cool interactive alignment and tree viewing, as well as
parsers for many file formats. I haven't looked too carefully at the source
yet, but it may be of use to biojava.
-Robin
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]On
Behalf Of Dickson, Mike
Sent: Thursday, March 08, 2001 3:21 PM
To: 'Matthew Pocock'; [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: RE: [Biojava-l] Parsing Code for Phylogenetic Trees
Is there any reason the phylogenetic tree stuff or the expression work
couldn't migrate into biojava?
Mike
-----Original Message-----
From: Matthew Pocock [mailto:[EMAIL PROTECTED]]
Sent: Thursday, March 08, 2001 6:18 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Parsing Code for Phylogenetic Trees
[EMAIL PROTECTED] 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
(http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser/
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,
Matthew
>
> -John
>
>
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