BIRCH

BioLegato: 

How do I use bioLegato?
Oct. 21, 2014
All tasks in bioLegato are done in four steps:
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".

bioLegato 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 bioLegato (eg. sequence data, phylogenetic trees, lists of GI numbers etc.), it will be launched in a new bioLegato instance window.


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