To do this, you need to specify the -keyalg RSA option when using keytool. For example, when you create the private key, stipulate RSA as the key algorithm:
keytool -genkey -alias test -keyalg RSA
Then when you create the certificate request, stipulate RSA as the signature algorithm:
keytool -certreq -alias test -sigalg MD5withRSA
keytool -import -alias [keyentry alias in keystore] -trustcacerts -file mythawtecert.crt -keystore [keystore name]
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