TUTORIAL: GDE Overview

GDE was originally designed as a multiple sequence alignment editor. However, the capability that makes it almost unique among bioinformatics programs is its ability to run other programs by generating Unix commands. Because it is designed to make it easy to add new programs, there is almost no limit to the kind of tasks that GDE can be programmed to do.

GDE is the primary graphic interface for launching programs in BIRCH. For each program, GDE provides a menu that lets you set program parameters, launch the program, and view the output. GDE takes care of all of the background details, such as translating files from one format into another. In many cases, output also goes to a new GDE window, making it possible to do ad hoc pipelining. This is one of the most powerful aspects of GDE, because it means that you can usually run additional programs using the output of one program as the input of the next. In contrast, most browser-based applications display output in a human-readable form that allows no further analysis by other programs.

How do I use GDE? - A brief introduction to how the GDE interface works.

One program; many data types - There are four GDE interfaces:

GDE - DNA/protein Sequence data
dGDE - lists of data items
mGDE - molecular marker data
tGDE - phylogenetic tree data

How does GDE work? - Everything that GDE does is accomplished by running external programs

GDE File formats

Pipelining using GDE - combining many tools to accomplish a complex task.

GDE 2.2 Manual (PDF) - This manual describes the nuts and bolts of the GDE program itself, NOT the programs that it runs. Almost all of the programs added to GDE (eg. BLAST, TCOFFEE etc.) were added as part of BIRCH. This manual was written for the original GDE 2.2 by Steven Smith. Most of the features it describes are described, but new features added in GDE 2.4 and later are not covered.