MacGDE: Genetic Data Environment for MacOS X
This product is not made by nor endorsed by Apple
If you don't see the button frame above click here.

Here GDE is NOT running on an external server and sending the display back to the Mac.
It is indeed running on the Mac under X11.

MacGDE and all of its components are now UNIVERSAL (PPC/Intel).
Thanks to Scott Buchanan (www.4dneuroimaging.com) for
supplying the universal XView libraries.
Thanks to Dr. Logan Donaldson for making the package installer for the libraries
(http://dryden.biol.yorku.ca/macosx/index.html).

See listing for MacGDE 2.3 at Apple or MacUpdate Web site.


"Push" the menu buttons to see all of your options
NOTE: to make the menus "fall" in the program Command(apple)+click

Updates 07-01-06.
Updater from 2.2 to 2.3 now available

Changes from 2.2 to 2.3

Changes to MacGDE the program:

"Protections" shortcut key changed from <shift-meta P> to <shift-meta R>
because of conflicts with some users setup.

"GenBank Submission" under the "File" menu now generates a
degapped FastA file with only the short name after the > and no extra data,
which was not useful for submissions anyway.

Changed the default location GDE's "Open" and "Import" commands
temp files from /usr/tmp to /tmp. This was to allow the default location to be the same
on all UNIX, Linux and MacOS systems. Therefore, the creation of the /usr/tmp folder
on MacOSX is no longer required.

"Make Mega, POY or SimPlot File" under the Phylogeny 2 menu can make any of
these three formats required by their respective programs. SimPlot uses FastA, where POY uses
a modified FastA (no > and a return between sequences) and Mega uses its own format
(# instead of >, and #MEGA as a first line with !Title "Filename" ; as the second line).
This command makes all three formats with their specifics now, NOT just a FastA file to be modified by hand.

Changes to accessory programs:

Added Inverted color output to MView, so the base letter is white and the background is colored.

Added Phyml 2.4.5 under the Phylogeny 2 menu.

Updated Blast to 2.2.14 which is now Universal.

All parts of MacGDE are now Universal!

GDE (MacGDE) is a set of programs for multiple sequence alignment and analyses. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and amino acid sequences, text, and masking sequence, and three forms of color highlighting. The system has several external analysis functions included for such things as automated alignment, searching, homology recognition, and phylogenetic analysis.


The requirements are MacOS X 10.3 (Panther) or 10.4 (Tiger) 10.3 or better RECOMENDED, X11 and a few xview libraries. I am using Apple X11.app (version 1 for Panther) but it should run under XDarwin with XFree86 4.2.1.1 with a windows manager such as OroborOSX.


GDE was initially ported to the Macintosh by BioLateral (contact Tim Littlejohn with questions about the port) as part of their efforts to bring Unix bioinformatic programs to the Macintosh platform as BioinforMac. In fact, a good way to get many Unix programs already ported to MacOS X in an installer package is to purchase their packages. Otherwise you can download and compile them yourself from various internet sources.

Disclaimer: I, Eric W. Linton, have no vested interest in BioLateral. I am just distributing GDE for the Mac (MacGDE) for the company since GDE's public license prohibits commercial enterprises from distributing GDE, even for free.


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Please report problems to lintone@msu.edu
The GDE for Macintosh Edition (MacGDE) is maintained by: Eric W. Linton, Research Associate
Plant Biology Labs, Michigan State University, East Lansing, MI, USA.
Site last updated July 01, 2006