These two programs implement ideas described by Z. Zhang, P. Berman, T. Wiehe
and W. Miller in the paper "Post-processing long pairwise alignments",
Bioinformatics 15, 1012-1019.  In particular, all experiments described
therein where performed using them.  However, be warned that they are in no
way intended to be "production quality" software.  Rather, they seemed (just
barely) good enough to validate some theoretical conclusions.

The program called "decom" simply converts one alignment file to another, by
removing alignment segments of very low score.  The program called "decomT"
produces the tree of "all decompositions", as descibed in the paper.  The
programs assume the alignment-scoring parameters
	match=10, mismatch=-10, gap of length k = -60 - 2k
but these can be reset on the command line, as in
	decom alignments I=-8
(I is the penalty for transitions, V is for transversions).

To compile them, you will need to obtain and install the "blastlib" library
that accompanies our sim4 program.  Also, alignments need to be in the format
used by our alignment tools, such as the sim (AKA sim96) program.

One set of test data is included here, consisting of the files:
	elegans - genomic sequence data from C. elegans
	briggsae - genomic sequence data from C. briggsae
	alignment - an alignment of the elegans and briggsae sequences computed
		using the Smith-Waterman criterion for local alignments
	decom.out - file computed by the command
			decom alignment Y=2000 > decom.out
		The Y parameter limits the amount that a segment of the
		alignment can score, in this case to -2000.  Alignments here
		are scored match=10, mismatch=-10, gap of length k = -60 - 2k.
	dotplot.pdf - PDF file giving a dotplot view of the files called
		"alignment" and "decom.out".
	decomT.out - file computed buy the command
			decomT alignment T=1 > decomT.out
		The T=1 flag asks for a particular format of output.  Here,
		we get a file starting with

8146 12331-58917 --->  12331-30146  31489-32158  32284-32359  33208-33333  34960-35167  36856-58917
2858 12331-30146 --->  12331-17556  19702-19806  20344-30146
1996 12331-17556 --->  12331-15559  16204-17556
1110 12331-15559 --->  12331-13182  13768-15559

		This shows the vertices at the top of the tree.  For instance,
		the root corresponds to score 8146, where five subalignments
		are joined to give an alignment covering positions
		12331-58917 of the first sequence.  The left-most child of the
		root, corresponding to positions 12331-30146, is formed when
		three subalignments coalesce at score 2858, and so on.  Thus,
		each node of the tree is represented by a line in the decomT
		output.  The X paramter can be set to a high value of one wants
		only the top part of the tree; nodes of score < X are not
		printed.