Methods 20180125

[alimanfoo]

This PR has some work on methods, plus misc edits to main text.

• Fix biber warnings in refs.bib
• Add a footnote to table 1 to explain domain nomenclature
• Some edits to existing methods
• Added methods for positive selection and assay design

Resolves #131.

[alimanfoo]

Hi @cclarkson, this is ready for review.