Sequence alignments:

Global alignments (align complete sequences against each other)
Local alignments (find optimal substring alignment(s))

Weighted (uses a weight matrix with the cost of substitutions)

\begin{code}

module Align

-- an alignment is a map of the characters to replace 
-- (the rest are deletions/insertions)
type PAlignment = (Array Int Bool) (Array Int Bool)

align :: Sequence -> Sequence -> PAlignment
walign :: WMatrix -> Sequence -> Sequence -> PAlignment


\end{code}