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According to Game Informer, Sega will publish Atlus USA games after the completion of its acquisition. From now on, all upcoming titles from Atlus will be released in North America by Sega of America.
Though Sega now owns Atlus, the Atlus name will remain in use and will continue to be independent, which for most fans, it’s great news.
Not just that, but since Sega made Atlus a member of its family, Atlus has used the Atlus experience to localize many games made in Japan for publication in the East.
[Source]: Game Informer: Sega Is Now Publishing Atlus U.S.A. Games, But Don’t Worry.