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To run VizBin double click the VizBin-dist.jar icon
Upon your first run, VizBin will initialize the settings.
This is how the main window looks like.
To specify the input sequences in fasta format, click on the "Choose" button
Navigate to the directory containing your input sequences in fasta format. Here, we have them in "Desktop/Data/"
Choose your file of interest, here EssentialGenes.fa
The path to your file of interest should now appear in the "File to visualize" box.
To star, simply click on the "Start" button.
Upon successful termination, a scatterplot will appear in which you will be able to select your clusters of interest. Please note that on different operating systems the resulting visualizations might differ but should be consistent qualitatively.
Now you can choose group of points that you want to export to seperate file. You can do this by drawing polygon. All points inside of this polygon will be exported. Each left mouse button click marks new polygon vertex. Vertexes need to be marked in clock-wise of counter clock-wise order.
To export points press right mouse button anywhere on window. Following window should appear
Press "yes", and choose directory where file should be saved and provide file name