SSH Certification Authentication
If you already have a private key from FTP server administrator, then you can simply enable "Certification Authentication" on "Profile wizard->FTP Server" and specify the private key file and password (if specified).
If you don't have one, you can also generate your own key pair and send the public key to FTP server administrator. You can use any standard tool to generate public and private key, such as PuTTYgen
SSL Certification Authentication
Similar to SSH, you can specify client certificate file when needed.
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