Installing CDSParser 1.0
Downloading CDSParser 1.0
To download CDSParser, click Download in the menu bar to the left to go to the McClellan Lab software download page.
Installing CDSParser 1.0
Unzip CDSParser.zip. There should be four files within the zip file: CDSParser.jar, clustal.def, defaults.def, and README. CDSParser.jar, clustal.def, and defaults.def need to be in the same directory for CDSParser to run correctly. Open the file clustal.def with a text editor and change the first line to reflect the location of ClustalW 1.83 on your computer. This can be the absolute pathname to the executable (/Users/.../clustalw), the pathname relative to CDSParser.jar (./clustalw1.83/clustalw) or the name if it's set up in your bin (clustalw). CDSParser also requires J2SE v 1.4.2 to run.
Running CDSParser 1.0
Once CDSParser 1.0 has been installed correctly, it can be run on commandline with:
java -jar CDSParser.jar
However, CDS will have to be in an active java directory if you are running in MS-DOS. This may require additional setup.