No they dont always use linux and they often leave backdoors to get back into your system. There's various ways of breaking and entering a system and there's also a wide variety of ways to cover your tracks, each depending on the attacker. As for the virii, There are virus assembly programs out there which program virii for newbies. An assembler is one of the things that you would need. Many viruses are written in C. A "Virus" is simply a piece of code that makes a system behave anormaly and often dealing damage to that system. A virus can be built to do whatever the builder wants it to do. If you're looking for more information also look up worms and trojans.

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