HELP - PHYLIP dataset too large for Excel!!

Brian Fristensky frist at cc.UManitoba.CA
Thu Apr 1 15:53:52 EST 1999


MERC wrote:
> 
>     I am trying to use RESTML on 37 taxa with 6 enzymes and about 600
> fragments.  I currently have each enzyme's data in Excel separately.
> This dataset, though, is too large to combine into one Excel file.  How
> can I put all of this data into one file so I can run RESTML?
> Thanks,
> Emily Latch
> Cedar Crest College
> 100 College Dr. Box #244
> Allentown, PA 18104-6196
> Phone: (610) 606-4968
> Fax: (610)606-4616
> Email: merc at cedarcrest.edu


I have written scripts that make it possible to run the PHYLIP
sequence programs through GDE. GDE is a multiple sequence
editor, intended for protein and DNA sequence data, but
it can handle text data. So discrete data, ie. the
presence or absence of bands or sites can be represented
as a sequence of 0's and 1's. You can download the .GDEmenus,
the scripts, and a Solaris version of GDE from:

http://home.cc.umanitoba.ca/~psgendb/index.html#SOFTWARE

Since GDE can handle sequences at least as large as yeast
chromosome III, your dataset is no problem.
The GDE menus currently can run the discrete data distance
methods (neighbor, fitch, kitch) as well as restml, which
uses maximim liklihood methods. By default, the PHYLIP
text output pops up in one window, and the tree pops
up in TREETOOL. 

GDE runs under most flavors of Unix, including Linux.

This package also runs most of the DNA and protein sequence
phylogeny programs from PHYLIP. I have found it tremendously
convenient to run PHYLIP from GDE.  Give it a try and let
me know if you have any trouble. 


-- 
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Brian Fristensky                | 
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frist at cc.umanitoba.ca           |  people who don't drink what a
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