The two source files in this directory are intervals.c and points.c.
Both build gap-free multiple alignments ("blocks") from a family of
pairwise alignments.  Intervals.c does so by treating each alignment
as a collection of "diagonal lines", while points.c treats an alignment
as a collection of points, i.e., pairs of matched sequence positions.
The output of the two programs is, at least in theory, identical.
In general, intervals.c should run substantially faster and in much less
space than points.c.  The two approaches are described in the paper
	W. Miller
	Building multiple alignments from pairwise alignments.
	CABIOS 9 (1993), 169-176.