This directory has a bunch of tools to create and visualize an
inferred alignment.  For example if we have three sequences, 
A, B and C and we wish to compare the inferred A/C alignment (from
the alignments A/B and B/C) to the real A/C alignment these tools
allow this to be done.  Here is breakdown of the scripts and programs:

(More details are obtained by running the c programs or looking at the
 comments of the perl programs)

 - transitivity.c:  This program (make it) takes two unpacked psl alignment
                   and creates a third one.  An unpacked psl is file which 
	           contains the output of pslUnpack.  This does the inference
                   of A/B and B/C to A/C.  

 - invert_coordinates.pl:  This program inverts the pslUnpacked coordinates.
                         The coordinates change from A B C D to C D A B.  This	                        creates the alignment B/A from A/B.

 - comparison_plot.pl: This program takes two alignments of A/B and creates a
		       a graph.  See comments at top of file.

 - expand_coordinates: This takes an unpacked psl and creates a the points from
		      the unpacked psl for use in comparison_plot.pl





