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This one doesn't seem to be able to ouput one single file https://superuser.com/questions/67721/how-to-encrypt-a-whole-directory-with-axcrypt-by-command-line-like-with-windows-c

Any other windows freeware which can do so by command line ?

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7-Zip, command line version (7za.exe).

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7-zip has a command-line interface. You can create an encrypted archive.

TrueCrypt also has a command-line interface, though I'm not sure if it's capable of archiving everything into a single file.

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You can also use tar to dump a directory structure to a file, then encrypt that single file with the tool of your choice.

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7-Zip is a good option.

In fact I liked it enough to write a batch file script that's 7-Zip-based (free / open source). Since it's all command-line, it's easy to schedule for creating unattended encrypted archives:

Ziparcy is a WINNT shell script that can be scheduled to create/update an encrypted zip/archive of your files (and directory structure).

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