how to make the phylogeny tree readable?

Jerry Learn learn at u.washington.edu
Fri Oct 24 12:44:59 EST 1997


In article <62oq2o$nde at net.bio.net>, "David F. Spencer"
<dspencer at is.dal.ca> wrote:

> 
> 
> Unfortunately 'treeview' has a maximum capacity of 200 taxa; the web site
> mentions that and I believe I've confirmed it myself.

Actually it appears that the limit is 500 so it should work with the
original poster's data set.
 
> The only solution that I've found to this problem, and I run into it
> routinely, is to use 'treetool' on a Sun. It hasn't been updated for quite
> a few years and needs a few code tweaks to get it built and working under
> Solaris 2 (the program dates from Solaris 1, SunOS's BSD days) but it
> doesn't appear to have any taxa limit. 'Treetool' accepts PHYLIP-generated
> treefiles and generates Postscript or PICT files on multiple pages; these
> file types can be edited quite easily, at least on Macs, but 'treetool'
> itself allows some editing of the tree so it may not be necessary to move
> the file to a different platform.
> 
> 'Treetool' source I assume is still available from the RDP web site at the
> University of Illinois, Urbana-Champagne and may be available at Don
> Gilbert's archive at Indiana.  Unfortunately 'treetool' can't be ported to
> other platforms, not even LINUX, because it comes with some
> SunSPARC-specific prebuilt static libraries that are used during
> compilation.  If anyone has found out a solution to this latter problem,
> say the source for those libraries, I would sure like to hear about it.

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.

Has anyone heard of any efforts to port treetool to java?  I don't have
the time myself and have not been successful in persuading others yet, but
I think that a java applet to build phylogenetic trees would be very
useful.

Jerry Learn

Research Associate

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