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Pros
Pro SSH Key Setting
Can set different SSH Key for each connection, whereas in CuteFTP it's set for the whole application.
Pro Visual compare
SmartFTP is capable of comparing two folders and display visually the differences between them.
Pro Has an integrated editor
SmartFTP has a capable integrated text editor with support for syntax highlighting, folding, auto-complete, brace and indent highlighting, utf-8 characters, etc.
Pro Interface similar to windows explorer
Pro Built-in tty
SmartFTP includes a terminal emulator.
Cons
Con Certain functionality is behind a paywall
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