Do Alternate Classes count for Favored Class Bonuses

[Feryn]

SInce a character who takes levels in ninja can't take levels in rogue, would the count as a rogue for things like the human favored class bonus of +1/6 of a talent or a dhampir's +1/2 to stealth and perception checks in dim light?

[Darigaaz the Igniter]

Yes. Just like archetypes, alternate classes still count as the base class.