how to make the phylogeny tree readable?

David F. Spencer dspencer at is.dal.ca
Thu Oct 23 19:28:08 EST 1997


In article <60oce7$kct at net.bio.net>, James McInerney <jamm at nhm.ac.uk> wrote:

> Michael Man wrote:
> > 
> > I have generated a phylogeny tree from a large set of sequences (250)
> > using PROTPARS and DRAWTREE programs in PHYLIP.  But the names of
> > sequences on my tree are too small to read.  I have tried to use different
> > font files without any improvement.  Can anyone suggest a better way or
> > different program to solve this problem?
> > 
> > Thanks.
> > 
> > -michael
> > 
> 
> Michael,
> 
> Presuming that you use either a mac or a windows machine, one of the nicest,
> mose user-friendly tree viewing programs is treeview.  It is available on the
> web from:
> 
> http://taxonomy.zoology.gla.ac.uk/software.html#Tree viewing
> 
> It will allow you to carry out a great many different tree manipulations that
> might serve to fulfill your requirements.
> 


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

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

--------------------------------------------
David F. Spencer, PhD
Dept. Of Biochemistry
Dalhousie University
Halifax, Nova Scotia
Canada

dspencer at is.dal.ca
dspencer at rsu.biochem.dal.ca




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