What are alternatives to Journal of Theoretical Biology? I am considering joining the recent boycott of Elsevier, however I work with biologists on theoretical/mathematical biology (in particular, evolutionary game theory and population biology). However, It seems like Journal of Theoretical Biology  is the premier journal for technical work in this field, and my co-authors often suggest it. 

What are some (preferably, open-access) alternatives to JTB?
There are quite a few journals where you can publish theoretical work in this area. Here are a few suggestions (the distinction is based on my perception and knowledge of what they've published, I'll let others chip in if they disagree):

For more theoretical work:


The IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).
The Journal of Computational Biology.
The Journal of Mathematical Biology.
The Bulletin of Mathematical Biology


For more applied work:


Bioinformatics.
BMC Bioinformatics. (open access)
Algorithms for Molecular Biology. (open access)
PLoS Computational Biology. (open access)


This is not exhaustive of course, and I suggest you discuss these "candidates" with your collaborators.

EDIT: I marked some of them "open access" because they advertise(d) so. This does not mean that the others do not offer that option, you'll have to check.