GDE2.2

Steven Smith smith at nucleus.harvard.edu
Sat Sep 18 12:16:30 EST 1993


The Genetic Data Environment version 2.2

Well, here it is.  The long overdue update to GDE 2.0.  This is
a maintainence update fixing several bugs, and adding a few features to
the core alignment editor, as well as updating all of the external
functions.

You can get the programs using gopher to megasun.bch.umontreal.ca.
Get the file GDE2.2.tar.Z, and one of the manuals (text, postscript or
MS Word for the Mac), pick a directory to install it (like /usr/local/GDE).
Then do the following:

demo# mkdir /usr/local/GDE
demo# cp GDE2.2.tar.Z /usr/local/GDE
demo# cd /usr/local/GDE
demo# zcat GDE2.2.tar.Z | tar xvf -
demo# rm GDE2.2.tar.Z

Have each person interest in using GDE add the following lines to their
.cshrc file...

set path = ($path /usr/local/GDE)
setenv GDE_HELP_DIR /usr/local/GDE/GDEHELP

...and type 'gde' to start it.


Here is what's new with GDE2.2:

Updates of the following programs:
Phylip (3.5)
Readseq
Treetool (check this one out)
Looptool
Blast
FastA

Updates of the following functions:
Translate
Printing

GDE now can write colormap files as well as read them.  There is also
a new "yanking" feature to the editor (kudos to Scott Ferguson, Exxon Co.).
Type <ctrl> k/l to yank bases from the left and right.  There is also
a new widget for the .GDEmenus file called choice_list to avoid those
huge menus.

Bug fixes include:

Selection mask problems (fixed in 2.1)
Circular sequence handling
"Relaxed" Genbank format interpretation
Several memory leaks.

This version was compiled under SunOS 4.1.2, Openwindows 3.0, and
the standard Sun C compiler.  It does work with Solaris 2.2 if
you put /usr/ucb in the front of your path.  The users manual has
been updated for 2.2, but I don't expect any real surprises for
most users. Let me know if you run into any difficulties.

As usual, I am completely indebted to all of the people who have
given me assistance with this release. Off the top of my head,
I would like to thank:

Tim Littlejohn for his work with the MegaGopher.

Chunwei Wang, and Erik Bunce for the updates and additions from Harvard.

Don Gilbert, Xiaoqio Huang, Joe Felsenstein, Bill Pearson, The good
folks at NCBI, Michael Zuker, Des Higgins, and Mike Maciukenas for the
inclusion of their programs in GDE.  And thanks to Carl Woese, Gary Olsen,
Walter Gilbert, and Pat Gillevet for all of their help in making this
software possible.


Steven Smith
Millipore Imaging Systems
smith at bioimage.millipore.com




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