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I've had malwarebytes and Avast or AVG coexist quiet nicely for years. Malwarebytes is specific for malware not viruses...Malwarebytes does not scan for viruses - Malwarebytes Anti-Malware Free utilizes Malwarebytes powerful technology to detect and remove all traces of malware including worms, trojans, rootkits, rogues, dialers, spyware and more ( http://www.malwarebytes.org/products/malwarebytes_free/ )

Malwarebytes Anti-Malware is not meant to be a replacement for antivirus software. Malwarebytes Anti-Malware is a complementary but essential program which detects and removes zero-day malware and "Malware in the Wild". This includes malicious programs and files, such as viruses, worms, trojans, rootkits, dialers, spyware, and rogue applications that many antivirus programs do not detect or cannot fully remove. It is important to note that Malwarebytes Anti-Malware works well and should run alongside antivirus software without conflicts. In some rare instances, exclusions may need to be set for your specific antivirus product to achieve the best possible system performance. http://helpdesk.malwarebytes.org/entries/20818081-Does-Malwarebytes-Anti-Malware-replace-antivirus-software-

Here's a good list of tools and some good information http://www.bleepingcomputer.com/forums/t/405/antivirus-antimalware-and-antispyware-resources/

edit to add: yes, both programs check the same file but they check it for different things...one looks for apples and the other looks for oranges. I've had users get malware and viruses from facebook and youtube. Keep in mind, my client base is residential not commercial.
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Posted by PurpleSkys
Updated - 11th Feb