can anyone tell me how I can cite the following MATLAB document?
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The actual form would depend on which bibliographic format you are following but:
MathWorks, (2012). Bioinformatics Toolbox: User's Guide (R2012a). Retrieved July 14, 2012 from www.mathworks.com/help/pdf_doc/bioinfo/bioinfo_ug.pdf
You should add a registered trademark symboal after MathWorks and trademark (TM) after Bioinformatics Toolbox.