[Pipet Devel] interesting...

J.W. Bizzaro bizzaro at bc.edu
Mon Mar 22 16:10:52 EST 1999

Thomas.Sicheritz at molbio.uu.se wrote:

> We could adapt the rotating/zooming idea to the python phylogentic tool
> (pyphy or phypy .. or physpampy ?)

Or how about locus_phy  :-)

> 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.

I'll  help all that I can!

> 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 do like the representation Peter showed us:


There are numerous ways people have chosen to represent this type of data.  I think a good
look at some of the literature will help us.  I'll see if I can find anything else.

> 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.

Phylogeny is something we be very concerned with in developing LocusML.  Your input to Justin
and Rahul would be helpful.

> 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 ?)

I wish.  I haven't heard of Bioinformatics'99.  Do you have a URL?

Konrad, will you be at RECOMB99?

> 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.

If you wish.  Be sure to work with Tim on the basic sequence tools, as he has been developing
some (Codon).

bizzaro at bc.edu

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