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Animated content is both simpler and more complicated.
Drawn content (eg: anime) is much easier to deinterlace, so you can use less complicated algorithms (like yadif) and still get very good results.
On the other hand, anime tends to have an effective frame rate of around 15fps, despite TV shows being broadcast at 29.97fps. So you may need to work out the correct frame rates to get rid of any ghost frames.
This of course will vary depending on exactly where the animated content is from (different animators have different publishing standards), and how exactly it's packaged (DVD/NTSC is always 29.97fps, different broadcasts could have different frame rates, etc).
meGUI is capable of pretty much anything you throw at it, so it stands that MeguIV can also handle it. But TGMC (MeguIV's main feature) is really intended for IV content so it would be overkill for animated content.
Sorry for the long-winded answer. The short end is, yes with a couple catches, but it's probably overkill so if you're serious about encoding animated content, you may want to give regular meGUI a go.
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