Is it a good idea to submit to a single-blind journal when I have no affiliation? I am looking to publish a paper in computational biology. However, I have no affiliation (I have been affiliated with some institutions in the past, but am not currently affiliated with anyone now). I am also looking for a journal that will publish with no charge as I am low on funds.

I understand I should be able to publish a paper when my work is evaluated solely for its quality. However I have been unable to find any non-predatory and at least semi-legitimate computational biology journals that use double-blind review and are free to publish in. 

I will submit my manuscript to bioRxiv, but would really like to publish in a journal. I am unsure how to proceed - should I try and submit to a single-blind journal and mark my affiliation as "independent scholar" or try some other way to publish to a double-blind computational biology journal?
Well, you have the following options:


Write up and publish your article as an independent researcher. If your work is theoretical and mathematically provable then, there is a high chance that the lack of affiliation doesn't affect the way the editor approach your paper. However, if you are using a large volume of data and providing surprising results, then there is a high chance that your lack of credit (if I may assume it.) discourages the journal from publishing your work. The fact is that most of the journals cannot dig down and verify the reproducibility of large-scale analyses so their best bet is relying on the credential of institutes.
Approach a PI in a related field to review your work and see if he can provide some feedback/comments on that. You can revise your manuscript based on your mutual discussions and add some potential experiments up and then publish it together. You probably would save a huge amount of money as you can depend on their funding resources.