How to mention an implementation tool in thesis?
It somewhat depends of the publication style that you use for your thesis. For example, APA (6th edition) does not recommend to cite standard office software and programming languages.

Therefore, if you would follow the APA guidelines, you'd just mention Python everywhere you need without citing any sources, however, you'd have to cite the MATLAB software. See the "Computer Software/Downloaded Software" section in APA Style Guide on electronic sources for an example of how to format software references. Applying this style, I came up with the following citation (note it's a hybrid of the two approaches, due to my attempt to accommodate the company's geography):


  MATLAB. (2012). MATLAB (Version 8.0) and Statistics Toolbox (Version
  8.1) [Software]. Natick, MA: The MathWorks, Inc. Available from http://www.mathworks.com/products/matlab


Please note that citing MATLAB, following some other publication styles, such as Chicago, is discussed in this blog post. If you use LaTeX to create your thesis, this blog post can help.