initial commit of my branch
replace Main
fix some bugs
linkage switch actually does something
start adding better usage messages
proposed simplification using orphan instances
small cleanup
switch to affine gap algorithm (but with linear gap penalty) since it returns both score and alignment
improve README
lift distance function out of main
fix default options
improve documentation and .cabal
fix README formatting
Merge pull request #3 from bcdarwin/master

merge mvp