MacGDE 2.3 review
DownloadMacGDE is a set of programs for multiple sequence alignment and analysis.
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MacGDE is a set of programs for multiple sequence alignment and analysis. 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.
What's New:
Changes to MacGDE:
"Protections" shortcut key changed from to 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 Mac OS X 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.
Requirements:
Mac OS X 10.3 or later
X11 Windowing environment.
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