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Hacking using Nikto and how to prevent it

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Last Modified: 2020-11-15
Hi,
Recently there is a case where one of the servers of company was hacked. (Its a startup)
I dont know the complete information yet ( but its like hacker is using some PHP thing to do it)
But it was like the hacker used something like Nikto software.
How does one prevent such kind of things. Its like there is a backdoor (I dont know what does that means and what i know the hacker can still enter the system even after the username and password is changed) and the hacker it seems still can enter into the domain or some machine and corrupt the database ?
Dont know how he can do that... Is that some ports are open etc ??
How to go about handling or fixing this.

I could think of few things but they are pretty elementary need expert inputs
1) Create some ssh login that is key  and password based
2) Find these open ports or what is this backdoor entry and fix it.

Thanks
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