2 Layer Authentication FTP?
What is the best way to prevent being hacked due to keylogging/ malware?
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Do not use FTP. See How To Use Filezilla to Transfer and Manage Files Securely on your VPS and/or How To Use SFTP to Securely Transfer Files with a Remote Server.
Disable password logins. See How To Create SSH Keys with PuTTY to Connect to a VPS.
Disable password logins. See How To Create SSH Keys with PuTTY to Connect to a VPS.
This tutorial runs through creating SSH keys with PuTTY to connect to your virtual server.