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: http://industry.ebi.ac.uk/~alan/BioWidget/ 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). Jeff bizzaro at bc.edu