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how to make the phylogeny tree readable?

David F. Spencer dspencer at is.dal.ca
Mon Oct 27 09:28:17 EST 1997


In article <62qmqr$mef at net.bio.net>, Jerry Learn <learn at u.washington.edu> wrote:
>In article <62oq2o$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.

As Jerry has pointed out, the latest version of 'treeview', 
released about last March, now accepts 500 taxa.  The main web 
page for 'treeview' still gives 200, but the online help (which 
uses your web browser to connect you to the 'treeview' site) has 
the higher number.

Although the newest Mac version imported my 270 taxa file and 
could change the tree type, etc., the whole tree was compressed 
into about a quarter-page chunk in the centre of one page; the 
help says trees can be printed over more than one page but I 
couldn't get the tree to be expanded to do this.  The program 
exports PICT format and further processing in a drawing program 
may be required to convert the tree into a readable printed form.

>> '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.
>

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).

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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