If Matthew's classpath doesn't work, also try CLASSPATH=c:\biojava\biojava\biojava-1.21.jar;c:\biojava\bytecode-0.90.jar;c :\biojava\xerces.jar;. I'm not sure how windows handles multiple '.'s in a file name, you may have to rename the jars to biojava.jar and bytecode.jar.
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