If you've got a shitload of footer links there's a good chance that's what caused your penalty. Disavow works but it's only as good as your best guess. There's also a fine line crossed between those links helping you and hurting you, so you may find you don't come back as strong as before those links set off any flags.
With the information given, I probably say go for it, but don't overdo it. Like other people mentioned the alternative is to build the link profile up so the bad links don't outweigh the good, but you have to consider that's going to be time consuming while disavow won't and weight the cost/benefit of it all.
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