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Phred is a base calling program for DNA sequence traces developed by Drs Phil Green and Brent Ewing at the University of Washington. Phred reads DNA sequence chromatogram files and analyzes the peaks to call bases, assigning quality scores to each base call.

Phred is free for academic use but does require registration and for you to obtain a licence. Please visit the Phred homepage and follow the instructions. A copy of the Phred source code will be sent to you by email. (Please note, processing Phred licences at the University of Washington can take up to two weeks)

You will be sent two files by email, and the one you need is called 'phred-dist-020425.acd.tar.z' To use Phred on Windows please follow the instructions below instead of those included in the email.

Installing Phred for Windows is a 2 stage process and we provide a complete walkthrough below. Screenshots can be viewed at various stages by clicking the icons to the right.

1) Compiling the code.
2) Setting the Environment variable.

Compiling the code

1		Once you receive the Phred source code, you should extract (typically using WinZip) the files into a folder where you would like to keep the software. We recommend creating a folder on your C Drive called Phred.
		Into that directory you also need to replace a file with a Windows specific file that will allow Phred to be built successfully. Please click here to download a zip file . Please unzip this file into the directory where you have just extracted Phred. Should Windows prompt "would you like to replace the existing file" Click yes.' If you do not have Winzip installed you can download by clicking here
	2	To install Phred you will need to download and install Microsoft's free Visual C++ Express Edition. Instructions for installation of which can be found here Please note you can accept the default installation values for Visual C++ and do not need to register.
3	Once installed, run the "Visual Studio 2005 Command Prompt", by selecting the relevant icon from your windows Taskbar start menu - see screenshot
4	Once opened you need to navigate to the directory where you have extracted the Phred source code (e.g C:\Phred) For example, if you have extracted the Phred source code into the directory 'phred' located on your C Drive, then the command would be: cd C:\phred (press return) Now type nmake (press return). Phred is now being compiled and you will see the progress on screen - once complete (you will see the command prompt) a file called phred.exe has been produced in the Phred directory.. You may now close down the Visual C++ Command Prompt.

Setting the Environment Variable

1	Using windows, go to the control panel
2	If using Windows XP click 'Start' - 'Control Panel' and (if neccessary, change the view to 'classic view'
	if using Windows 2000 click 'Start' - 'Settings' - 'Control Panel'
3	Double click 'System', which will show up a window containing many TABS. select the tab marked 'Advanced' and then click on 'Environment Variables' towards the bottom
4	Click 'New' located below the System variables box (not user variables) .
5	Enter the following in the 'New System Variable' popup box, replacing "C:\phred" with the location you have saved phred if different. ( please enter exactly) Variable : PHRED_PARAMETER_FILE Variable Value : C:\phred\phredpar.dat
6	Click 'OK' to continue Click 'OK' in the Environment Variables dialog Click 'OK' in the System Properties dialog.

You have now successfully installed Phred for use on your PC.

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