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#General Notes on Bioinformatics  ##Command Line/Terminal Tutorial  This workflow is written assuming that the user is using a computer running  Mac OS  or Linux. It is possible to perform much carry out many of the computational parts  of this workflow in a Windows environment but would require details getting these steps to work in Windows is  outside the scope of this project. Some parts of this workflow requireuse of  the UNIX user to provide text instructions for software programs by using a  command line. line interface.  While potentially intimidating to computer novices,  the first-time user, we use of command line interfaces is sometimes necessary (e.g., some programs do not  have attempted to provide all graphical interfaces) and is also sometimes much more efficient. To access  the information required command line on a Mac navigate  to run scripts or software in this environment. Applications > Utilities > Terminal (THIS SEEMS AWKWARD -- WHY NOT SAY "OPEN THE TERMINAL PROGRAM IN THE APPLICASTIONS FOLDER")  To access the command line on When this application is launched  a Mac navigate to Applications > Utilities > Terminal  A terminal new  window will appear. This is known as a "terminal" or a "terminal window."  In the terminal window, you can interact with your computer without using a mouse. Many popular programs in common use have a GUI (Graphical User Interface,) but many of the ones used in this workflow will not. So, instead of double-clicking to make a program run, you will type a command in the terminal window. We will walk you through how to run all of the programs required for this workflow, but you must first acquire a basic familiarity with how to interact with your computer through the terminal window. Below is a list of commands that will be required to use this workflow. There are many tutorials available to help you get started. For more information on operating in the terminal, check out  this video: