[Pipet Devel] interesting...

[Thomas.Sicheritz at molbio.uu.se]

Tim writes:
 > http://www.inxight.com/Inxight_Corporate_Web_Site/Edu_Org_Program/Intro_to_Program.html
 > 
 > Take a look at this tool...  looks like it could be useful for browsing
 > phylogenetic trees.

Hmm ... :-) ... it looks quite fun ... (look at the spider phylogeny)
We could adapt the rotating/zooming idea to the python phylogentic tool
(pyphy or phypy .. or physpampy ?) 
Actually I really like the idea ... phylogenetic reconstructions tend to get 
large amounts of taxa - which is not easy to see in one window.
I have to write a treeviewer module for my (hopefully) last bigger project
(phylogenomics) in my thesis. I thought I would hack it in Tcl/Tk but with
some help from other loci'ers I could try it in python.

There is no good treeviewing program for all platforms (read: nothing for
Linux and Solaris which doesn't need 8bpp color mode)
I always had some problems to code treeparsing scripts and beeing able to
represent them in a "good" way on the screen (trifurcation, distances etc.)
I could need some help here ... 

I started on some smaller versions where the branches or taxa labels (in my
case SWISSPROT ID's) are linked to yank (sequence retrieval), SWISSPROT
database, blast and clustalw - which should be connected/linked from the
whole genome map/sequence ... that seems to fit perfectly into the LOCI
way of thinking.

My time schedule:
* mar,apr,may: finish my current paper 
* apr: bioinformatics meeting in Lyon(France)  (RECOMB99)
* apr: bioinformatics meeting in Lund(Sweden)  (bioinformatics'99)
  (am I going to meet some of you in Lyon or Lund ?)
* ???: start with the phylogenomic project

I am very tempted to leave the whole sequence editor part to Dave and
only keep on with the basic_nucleotide_sequence and phylogenetic tools.

Suggestions ?

-thomas

-- 
Sicheritz Ponten Thomas E.  Department of Molecular Biology
blippblopp at linux.nu         BMC, Uppsala University
BMC:  +46 18 4714214        BOX 590 S-751 24 UPPSALA Sweden
Fax   +46 18  557723        http://evolution.bmc.uu.se/~thomas
Molecular Tcl:   http://evolution.bmc.uu.se/~thomas/tcl
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