Can anyone recommend a computer program that can help me with this...

[max_planck735]

I'm trying to find a computer program that will let me input a set of notes, and which will then produce a list of the scales that contain those notes.  Hopefully the set of scales that the program searches through will be very comprehensive.  Does anyone know of a program that can do this?

[prometheus]

The list of scales is endless. And the same set of notes have many different scale names. I don't really see the point.

Isn't the nature of the intervals more important than the many names people give the scales?

[ted]

As part of an algorithmic fugue effort I did years ago I remember writing a subroutine which analysed simultaneous, or nearly simultaneous groups of pitches into partitions of the chromatic scale. Since some partitions occur all the time in conventional music and others hardly ever, it seemed a good starting point, and to a certain extent it worked surprisingly well.

As this sort of thing is heavily dependent on your specific goal, I suggest you obtain a compiler and write your own code. You don't need a huge learning curve with C or anything like that. Get a fast, comprehensive Basic such as BlitzPlus, which can be learned in a few hours. Blitz is actually ideal for algorithmic music because it has excellent control over sound as well.

https://www.blitzbasic.com/

[quantum]

This isn't exactly what your asking for but it deals with scales, tunings, temperaments and microtonality. 

Scala:
https://www.xs4all.nl/~huygensf/scala/

The results your particular question can produce are very large.  Is there any particular reason you want to do this, or can you further refine your query?

Similar with Ted's response, you may be interested in Pure Data (PD) which is a graphical programming environment ususally used for music, video and other multimedia.  It is similar to MAX/MSP but is free.
https://puredata.info/