Applying for PhD after a poor master's
Delay applying for a year and work on a new project, where you can perform much better (now that you have more experience). Get a publication out of that and work with someone new, who will write you a good recommendation letter.

I know for a fact that many labs are very interested in getting bioinformaticians, so it shouldn't be hard if you are not looking for a great salary (which you shouldn't be: this is a career investment).