jpayne@69: -- Version history --
jpayne@69: 
jpayne@69: 3.23 - Added -D and --banded option to nucmer. These options can be used to
jpayne@69:        specify the largest indel that will be included in an alignment
jpayne@69:        segment without breaking it in two pieces.
jpayne@69: 3.22 - Significant 'dnadiff' bug fixes. Breakpoints, unaligned seqs, and
jpayne@69:        SNP counts now reported accurately. Unaligned contig output format
jpayne@69:        switched to match show-diff format. Dynamic memory allocation for
jpayne@69:        run-mummer1. Turned off output of the near useless .cluster files
jpayne@69:        from nucmer and promer (let us know if you still want them).
jpayne@69: 3.21 - gcc compatability fix.
jpayne@69: 3.20 - Added 'dnadiff' comparative analysis script, 'show-diff' nucmer
jpayne@69:        utility, and fixed a number of build issues.
jpayne@69: 3.19 - Fixed gcc4 build problem	.
jpayne@69: 3.18 - Fixed bugs in delta-filter, began migrating to delta library.
jpayne@69: 3.17 - Many changes, major upgrade. Added/improved delta-filter, show-snps,
jpayne@69:        mummerplot, and mgaps. Multiplot capability added to mummerplot.
jpayne@69: 3.16 - Added 'delta-filter' utility.
jpayne@69: 3.15 - Fixed --nooptimize in nuc/promer.
jpayne@69: 3.14 - Fixed gcc3 compilation bug.
jpayne@69: 3.13 - Added -d, -g, -G and -o options to show-coords and updated
jpayne@69:        documentation. Fixed bug in show-tiling -R.
jpayne@69: 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed
jpayne@69:        a bug in nucmer and promer. Fixed rounding issue in show-coords.
jpayne@69:        Updated citations.
jpayne@69: 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
jpayne@69:        the issue with mummerplot being to faint.
jpayne@69: 3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
jpayne@69: 3.08 - Added MUMmer examples web docs which gives brief walkthroughs.
jpayne@69: 3.07 - Added the 'mapview' plotting utility and appropriate documentation.
jpayne@69:        Fixed origin wrap shadowing bug in show-tiling when using the -c option.
jpayne@69:        NUCmer and PROmer now convert to absolute paths to avoid ambiguity.
jpayne@69: 3.06 - Added -F and -h option to mummer. Changed -mumcand option to
jpayne@69:        -mumreference, but left deprecated -mumcand option available. Added
jpayne@69:        -maxmatch option to mummer, and changed default behavior of all
jpayne@69:        applicable programs to -mumreference (nucmer, promer and mummer).
jpayne@69:        Added -w (screen width) option to show-aligns. Updated documentation
jpayne@69:        with all of these changes.	
jpayne@69: 3.05 - Added -k option to show-coords to only display the best frame for
jpayne@69:        overlapping PROmer alignments. Added --[no]optimize option to nucmer
jpayne@69:        and promer to allow alignment score optimization to be turned off, i.e
jpayne@69:        allow alignments to extend to the ends of sequences rather than
jpayne@69:        backtracking to optimize the alignment score. Updated docs.
jpayne@69: 3.04 - Fixed combineMUMs bug and added new option, added some developer
jpayne@69:        support in the src/kurtz subdirectory, and added extra INSTALL
jpayne@69:        information in the docs.
jpayne@69: 3.03 - Added HTML user manual in the /docs/htmlmanual/ subdir.
jpayne@69: 3.02 - Fixed small bug in show-coords. Added additional options
jpayne@69:        to show-coords. Added extra help text to show-tiling. Changed
jpayne@69:        contact email address. Consistent padding added to combineMUMs.
jpayne@69: 3.01 - Fixed off-by-one error in multi-reference 'mummer' usage.
jpayne@69: 3.00 - Initial open source release!