[Pipet Devel] Re: phylogenetic gui using pygnome

[Thomas.Sicheritz at molbio.uu.se]

 > Rick Ree wrote:
 > > 
 > > Hi, I noticed your openlab entry on freshmeat the other day, and also that
 > > the pygtk tools website is hosted by you.  I've been working on some
 > > graphical ui tools for viewing/manipulating phylogenetic trees using
 > > python and pygtk/pygnome, and have an almost-beta prototype application
 > > that allows click-and-drag branch swapping, branch rotation, etc. a la
 > > MacClade.  It's more proof-of-concept than anything else.  Are any of your
 > > group interested in phylogenies?

 > Certainly.  We are actually trying to implement phylogenetics into Loci.  We'll
 > be defining an XML/DTD for it too.
 > 
 > The two guys on the Loci team who have the most interest in phylogenetics are
 > Thomas Sicheritz (Thomas.Sicheritz at molbio.uu.se) and Tim Triche
 > (jabbo at mindless.com).  At the very bottom of this message is a reply to Tim from
 > Thomas.  This may give you some idea about Thomas's interest.

Great - I am currently working on a basic treestructure in python - but if
Rick has the basic tools + the viewing/editing set ... and like to share it 
to theopenlab, I'll be VERY glad ! (I'd rather go directly on the
viewing/editing/manipulating part instead of messing around with treenode
parsing ...)

My current outline is:
* treenode class, reading/parsing NEWICK(phylip) and NEXUS(Paup) tree
  format
* allow for trifurcations !!! (very important, IMHO - most of UNIX tree
  programs can't handle multibranching nodes)
* basic tree manipulation like changing outgroup/nodes, fonts, Taxa names
  directly in the canvas, color-grouping by species/kingdoms
* parsing of rich NEXUS files with additional taxonomy information
  or direct linking to EMBL/SWISS/GenBank, NCBI's taxonomy browser, KEGG etc.
* different views (unrooted, cladogram, phylogram, fishview etc.)
* 2 displays - (whole tree and selected portion)
* colored alignment viewer/editor (ála seaview)
* basic picture editing tools like xpaint

This just happens to be closely related to my next project :-)
- so I can spend a lot of time with that.
If we get the basic structure working - then the rest should be rather easy 
(there is nothing new, just ideas and features from different existing
programs)

Rick - could you contact me directly ?

c ya
-thomas
-- 
Sicheritz Ponten Thomas E.  Department of Molecular Biology
blippblopp at linux.nu         BMC, Uppsala University
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