The field of bioinformatics is flourishing, and strong growth is only projected to continue. Like any cutting edge technology, bioinformatics requires an integrated IP strategy involving patent, trade secret, and copyright laws. The patent system in particular can be a powerful protection for commercializing bioinformatics inventions as long as a corresponding patent application meets certain patent law standards. Recently, the most rapidly evolving of these patent law standards—patent eligibility—came to a crescendo last year when the Supreme Court in Alice v. CLS Bank introduced a two-step test for determining whether computer-implemented inventions are patent-eligible. Since then, other courts and the USPTO have applied the test on inventions implemented on a computer and/or using the Internet with fact-dependent results. Here, we discuss how these decisions relate to bioinformatics inventions. We then analyze bioinformatics patents that have recently issued post-Alice. While the law remains relatively underdeveloped, it becomes clear that relying on a general purpose computer to perform routine or conventional steps in a claim will not infuse patent-eligibility into a claim. However, bioinformatics inventions remain patentable, especially when the patent prosecution team properly and persuasively presents the technical improvements and commercial embodiments.