It's not often that you see a developmental-stage biotech company's stock go up after it gets dropped by its pharma big brother, but Alnylam Pharmaceuticals (NASDAQ:ALNY) managed to buck the trend yesterday with a 4% gain.

Alnylam and Merck (NYSE:MRK) decided to end their four-year-old RNAi partnership and go their separate ways. As with all good divorces, the desire to split was mutual and will probably benefit both companies more than staying together ever could have.

The collaboration has been in turmoil since Merck bought Alnylam's rival, Sirna Therapeutics, last year. The purchase meant that Merck no longer needed much of the expertise that Alnylam brought to the table. Alnylam's partner was now also a rival, so helping out Merck might have resulted in competition in drugs developed outside the partnership.

The only real question is why the two didn't end the partnership months ago. While the dissolution of the partnership results in a loss of funding for Alnylam, it's not like the company has been left to go it alone. It still has partnerships with Medtronic (NYSE:MDT), Novartis (NYSE:NVS), Biogen Idec (NASDAQ:BIIB), and Roche. Last week, it also announced a joint venture with ISIS Pharmaceuticals (NASDAQ:ISIS) to develop micro RNA therapeutics.

The phase 2 clinical trial results from Alnylam's lead compound, ALN-RSV01, are due in later this year. If they are positive, Alnylam could score an additional partnership. But with an expected $435 million in cash at the end of this year, Alnylam could try to push into phase 3 clinical trials alone, especially if it can score a few more of those non-exclusive technology licenses like the one it has with Roche.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. Biogen is a pick of the Stock Advisor newsletter. The Fool has a disclosure policy.