how to make the phylogeny tree readable?

newsmgr at merrimack.edu newsmgr at merrimack.edu
Fri Oct 31 18:35:47 EST 1997


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Newsgroups: bionet.molbio.evolution,bionet.software
Subject: Re: how to make the phylogeny tree readable?
Message-ID: <63dpdo$ktc$1 at dismay.ucs.indiana.edu>
From: gilbertd at bio.indiana.edu (Don Gilbert)
Date: 31 Oct 1997 23:25:44 GMT
References: <62qmqr$mef at net.bio.net>
Organization: Biology, Indiana University - Bloomington
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NNTP-Posting-Host: chipmunk.bio.indiana.edu

You may want to look at the recently updated Phylodendron,
which is a Java application for drawing phylogenetic trees.

http://iubio.bio.indiana.edu/soft/molbio/java/apps/phylodendron-doc.html

It isn't yet comparable to treetool in all it can do, but
I'll try to make it that way over the coming months/years.
I also would welcome anyone else wanting to help or take over
working on the Phylodendron code.

Phylodendron has no explicit limit on taxa, but it currently gets
very awkward to use at the 200+ level.  It also suffers still
from some general awkwardness and user-interface "wobblies".

But it has several potentially useful features, including PICT,
Postscript and GIF output formats, tree and node style options.
If you test it out, send me mail suggesting what features from
TreeTool or other that you would most like to see added.

The tree drawing algorithms are based on Joseph Felsenstein's
DrawTree and DrawGram of a few versions back;  Phylodendron evolved
from the Mac hypercard stack TreeDrawDeck I wrote several years
back.

I took a look last weekend at treetool's source, but the diverence
of it from Phylodendron's java is too much to make introgression
likely at this point.
 
-- Don
 
In article <62qmqr$mef at net.bio.net>,
Jerry Learn  <learn at u.washington.edu> wrote:
>
>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.
------

--
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu




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