The best replacement for qualys is nessus.

The best alternatives to qualys are rated as following:
★★★★★  nessus
★★★★  nexpose
★★★★  rapid7
★★★★  veracode
★★★  webinspect
★★★  acunetix
★★★  foundstone
★★  whitehat

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No companions for qualys have been suggested so far.
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