Certificate Toolkit is available in the webMethods IS section (using Installer). For wM 4.6, it is a separate download, also in the IS section.
However, be prepared to spend some time with CertTK. It is very picky about the version of JDK/JRE you’re using, so be sure to follow exactly what wM wants you to do. It is known to work partially (e.g. generate CSR that doesn’t work) if JDK/JRE is not just right. My experience…
#webmethods-Protocol-and-Transport#webMethods#Integration-Server-and-ESB