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I know no one that works as of today (i.e., kernels not way too old) and I wonder if anybody found or knows any protector for Linux either commercial, open source, used in malware, etc...

joxeankoret
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ZVrba's Phrack article on cryptexec: Next-generation runtime binary encryption is a good read and it doesn't rely on additional kernel functionality:

This article describes a method to control the target program that doesn't does not rely on any assistance from the OS kernel or processor hardware. The method is implemented in x86-32 GNU AS (AT&T syntax). Once the controlling method is devised, it is relatively trivial to include on-the-fly code decryption.

0xea
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There is a nice article on Linux binary code protection at http://www.intel-assembler.it/portale/5/linux-binary-code-protection/linux-binary-code-protection.asp.

If your target is to protect your binary Sentinel HASP supports Linux.

As for the old ones as you mention most of them don't work anymore, elf-encrypter Shiva, Burneye etc. IF I had to guess what will be the most common in Linux malware it will be the most common packer that's is used in windows too, UPX.

Nicolas
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The majority of modern ELF binaries are protected using UPX or a variant thereof. 1,2 However, custom packers have been observed in the wild, including both UPX based- and non-UPX based-custom packers.




References

  1. Understanding Linux Malware

  2. Modern Linux Malware Exposed

  3. Unboxing Linux/Mumblehard (2015) - ESET

julian
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