1. Select data (eg.
sequences) 2. Choose a program 3. Set Parameters 4. Launch the
program
1. Select data - You can
either select names of data items, or the data themselves. Selecting
names is done in the name panel. Click on a single name, or drag across
a set of adjacent names. Names can also be chosen one by one by holding
the Shift key and clicking on names. Each time you click, a name is
either selected or deselected. Data can also be selected in the
alignment window. You can select a block of subsequences from an
alignment by dragging horizontally and vertically in the alignment
window.
2. Choose a program - Once
data are selected, choose a program from one of the menus. A parameter
menu for that program will pop up.
3. Set Parameters - The
parameter menu lets you specify parameters for running the program. For
example, a menu for a pairwise sequence alignment program might give
you a choice of scoring matrices to use, or to choose whether or not
gaps at the end of an alignment should be assigned a penalty score.
4. Launch the program - All
menus have an OK button. When you click on this button, the selected
data will be written to an input file to be used by the program. If
data have been selected in both the name panel and the alignment panel,
you will be prompted to choose whether you wish to use the "selected
sequences" or the "selected regions".
GDE will run the program using the selected data and the specified
parameters. When the program is finished, output will pop up in
windows, or, if specified in the parameter menu, written to a file.
When output is displayed on the screen, it is displayed using a program
appropriate for the output. If output is text, it will be opened in a
text editor; PDF output would be displayed in a PDF viewer (eg. Adobe
Acrobat); HTML output would be displayed in a web browser. When output
is data that could be read into GDE (eg. sequence data, phylogenetic
trees, lists of GI numbers etc.), it will be launched in a new GDE
window.
