Extract all files within the msa2v355matlab.zip file into a MASTAN2 folder on your computer. Start the MATLAB program and set the Current Directory to the location of this MASTAN2 folder. To avoid having to do this each time you startup MATLAB, you can permanently add this folder to the MATLAB search path by using Matlab's Set Path feature. After using either of these procedures, type mastan2 (only lower case letters with no spaces) at the MATLAB command line prompt (>>) and the MASTAN2 graphical user interface (GUI) should start. If the GUI does not start, and you get an error message that reads ??? Undefined function or variable mastan2, you have not properly set the current directory or path to point to your MASTAN2 folder.