It's all over, and in fact much of it is Muslim sect against Muslim sect.
A very recent article from
Janes talking about what is happening in Somalia and the Sudan and how Bin Laden definitely has designs on large portions, if not all, of Africa.
The Sudanese conflicts are largely the Northen Islamic peoples against the Southern Christians.
There is Muslim/Christian conflict all over Nigeria (though there are arguments that this is primarily over resources and that the battle for those scarce resources are bringing people together by religion to fight for them).
And an interesting find on Ethiopia from
Time.
While the roots of the conflicts are not always (or even usually) religious, Islamics leaders have oft been quick to latch onto the geopolitical situation and turn the ide into an effort to expand their influence through violence and intimidation.