The best replacement for nikto is nessus.

The best alternatives to nikto are rated as following:
★★★★★  nessus
★★★★  w3af
★★★  skipfish
★★  wikto

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Speaking about nikto, one probably shouldn't forget about nessus.

Other search terms related to nikto and their ratings are:
★★★★★ nessus
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Google Trends

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nikto
nessus
w3af