how to make the phylogeny tree readable?

Jerry Learn learn at u.washington.edu
Mon Oct 27 12:03:17 EST 1997


Do you have a list of the changes to the Makefile, or possibly the
Makefile itself that you could send to me?  I would very much appreciate
it.  I would be nice if someone could find a computer science student to
rewrite treetool in Motif (although I still like OpenWindows).  It is, in
my opinion, the best program for manipulating phylogenetic trees, although
it does have a few quirks that I'd like to see fixed.  At least it doesn't
crash the Xwindows display like it would frequently do under Solaris 1.  

About GDE, have you fixed it so that the meta-keys work?  That's the only
feature that I miss in the version that I use (ported to Solaris 2.x by RZ
and NJP).  Meta-g and meta-n work but that is it.  Also under Solaris 2.x,
the edit window "grabs" the focus in a very inconvenient fashion.  If a
dialog window opens  over the sequence part of the edit window, I can't
point to it without having the edit window jump to the top.  Does your
build have that same problem?

Any help that you can give would be appreciated.

Jerry Learn

Research Associate

Health Sci. Ctr., Rm. K443-C      |
Dept. of Microbiology             | Learn at u.washington.edu
University of Washington          | Phone: (206) 616-4286
Box 357740                        |   FAX: (206) 616-1575     
Seattle, WA  98195-7740  USA      |   

In article <6328e1$fcv at net.bio.net>, "David F. Spencer"
<dspencer at is.dal.ca> wrote:

> In article <62qmqr$mef at net.bio.net>, Jerry Learn
<learn at u.washington.edu> wrote:
> >Dave, have you tried just using the binary that was compiled for SunOS
> >4.1.x under binary compatibility mode -- I think that we use it right out
> >of the box without needing to tweak code.  I did hit a limit with a very
> >large dataset (~1000), but I think it was a limit in the display window. 
> >When I reduced the font to 8 pt, I was able to see the whole tree.  But
> >this implies that there may be a limit (about 1500?) to display trees in
> >"phenogram" format -- I don't even want to think about a radial tree with
> >>1000 OTUs.
> >
> I originally ran 'treetool' under Solaris 1.1 and may have used 
> the precompiled version at some stage before building my own.  
> When I upgraded to Solaris 2.4 I decided to rebuild things 
> properly to the new OS and that required modifications to the 
> source for GDE and 'treetool'.  My only disappointment at this 
> stage is that I can't find the source for the static libraries 
> 'treetool' uses during linking and so I can't build it for LINUX 
> (XFree86).
> Any further discussion of this would be more be appropriate I 
> would think in 'bionet.software' (and the moderators presumably 
> would agree).

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