When I was a teenager, I read a brilliant story where a group of children are living on an island and one of them is the daughter of a scientist who creates a GM crop (or a virus that does some thing to crops?) that goes out of control and causes all sorts of problems. They get quarantined by a group of uninfected(I don't know why they were uninfected, maybe it was a virus or perhaps the crop emitted something?) military living on a battleship, and the girl enters a whole kingdom of intelligent raptors divided into 'yes' and 'no' (though I can't remember what they had to do with yes and no); I'm not sure but I think one of these factions was yellow and the other was blue.
Any help leading me onto the right path would be much appreciated.