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As can be seen here and here, Thunderbird does not offer an option to select a more modern encryption algorithm than 3DES when sending S/MIME encrypted mail.

Is there any way to change this by using a plugin, modifying a config file, etc? Or is there any way to use Enigmail for S/MIME mails?

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At the time of writing, this is not possible in Thunderbird. A ticket for this is opened in 2003 and has not been resolved as of yet. However, patches with options for SHA-2 signing and AES encryption have been posted already. Please refer to bug #222179 for more information.

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