PokéBase - Pokémon Q&A
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Honestly don't know a lot about them apart from the fact that they edit Pokemon. I know this is a stupid question to ask, but considering I have little knowledge about them can someone please answer the following questions:

  1. What's the difference between Pokegen/ Pokesav and RNG Manipulation?

  2. Which of the two programs is better at creating and modifying Pokemon?

  3. Which one is easier to use?

  4. Which program is most difficult to detect for the Pokemon Company in tournaments when they double check for these particular Pokemon?

  5. Where can I find updated links for RNG Manipulation?

Thanks you!

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They are two completely different things.

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Yeah like JarJar said these relate to each other in no way possible
Pokegen (and variants) are programs used to create Pokemon and send them to your game via GTS. These Pokemon are 'hacked' and are not allowed to be used in any sort of official tournament and stuff.
RNG Manipulation on the other hand is perfectly legal, as it abuses your Ingame ID, and allows you to get IVs that you want (But it takes really long and stuff). You can click here for Smogon's RNG stuff. You can use Pokemon affected by these in whatever the heck you want

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Cheers for the info, do you know where I can find an updated link for the software for RNG?
Go through the smogon link I gave you, that should have the other settings and stuff required for RNG