I hope not, but they have filed one of those ridiculously broad, sweeping patents that covers a big chunk of basic techniques in the field:

The patent, filed by Microsoft researcher Steve Ozer in July 2007 and recently discovered by a graduate student at the University of Texas in Austin, claims ownership of several common phylogenetic methods. At its most basic, however, it seems to patent identifying any evolutionary relationship from sequences: “receiving a plurality of sequences across a plurality of species [and] mapping at least a portion of the plurality of sequences to an evolutionary tree.” 

The patent hasn’t been approved, and there’s a good chance it won’t be…but keep an eye on that evil empire in Washington state.