Hi. When running the "java seq.GCContent" command line, ensure that the 
classpath includes the current directory as well as all those in the 
compile-time classpath. e.g. on windows:

java -classpath %CLASSPATH%;. seq.GCContent

and some unix shells:

java -classpath ${CLASSPATH}:. seq.GCContent

See if that helps any.

Matthew

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