├── LICENSE ├── MUMmer3.23 ├── ACKNOWLEDGEMENTS ├── COPYRIGHT ├── ChangeLog ├── INSTALL ├── LICENSE ├── Makefile ├── README ├── aux_bin │ └── README ├── docs │ ├── Makefile │ ├── README │ ├── differences.README │ ├── dnadiff.README │ ├── mapview.README │ ├── maxmat3man.tex │ ├── maxmat3src.pdf │ ├── nucmer.README │ ├── optionman.sty │ ├── promer.README │ ├── run-mummer1.README │ ├── run-mummer3.README │ ├── skaff.sty │ └── web │ │ ├── MUMmer.pdf │ │ ├── MUMmer2.pdf │ │ ├── MUMmer3.pdf │ │ ├── XFiles.pdf │ │ ├── applications.html │ │ ├── compare.html │ │ ├── examples │ │ ├── data │ │ │ ├── B_anthracis_Mslice.fasta │ │ │ ├── B_anthracis_contigs.fasta │ │ │ ├── D_melanogaster_2Rslice.cds │ │ │ ├── D_melanogaster_2Rslice.fasta │ │ │ ├── D_melanogaster_2Rslice.utr │ │ │ ├── D_pseudoobscura_contigs.fasta │ │ │ ├── H_pylori26695_Bslice.fasta │ │ │ ├── H_pylori26695_Eslice.fasta │ │ │ ├── H_pyloriJ99_Bslice.fasta │ │ │ ├── H_pyloriJ99_Eslice.fasta │ │ │ ├── README │ │ │ ├── mapview_0.fig │ │ │ ├── mapview_0.pdf │ │ │ ├── mummer.fplot │ │ │ ├── mummer.gp │ │ │ ├── mummer.mums │ │ │ ├── mummer.ps │ │ │ ├── mummer.rplot │ │ │ ├── mummer1.align │ │ │ ├── mummer1.errorsgaps │ │ │ ├── mummer1.gaps │ │ │ ├── mummer1.out │ │ │ ├── mummer3.align │ │ │ ├── mummer3.errorsgaps │ │ │ ├── mummer3.gaps │ │ │ ├── mummer3.out │ │ │ ├── nucmer.cluster │ │ │ ├── nucmer.coords │ │ │ ├── nucmer.delta │ │ │ ├── nucmer.snps │ │ │ ├── nucmer.tiling │ │ │ ├── promer.aligns │ │ │ ├── promer.cluster │ │ │ ├── promer.coords │ │ │ └── promer.delta │ │ ├── dotplot.gif │ │ ├── examples_logo.gif │ │ ├── index.html │ │ ├── mapplot.gif │ │ ├── mapview_fig.jpg │ │ └── mummer_ps.jpg │ │ ├── index.html │ │ ├── logo.gif │ │ ├── manual │ │ ├── AlignmentTypes.odg │ │ ├── AlignmentTypes.pdf │ │ ├── covplot.gif │ │ ├── dotplot.gif │ │ ├── gaps.gif │ │ ├── index.html │ │ ├── manual_logo.gif │ │ ├── mapplot.gif │ │ ├── mgaps.gif │ │ ├── multiplota.gif │ │ ├── multiplotb.gif │ │ ├── nuc_proex.gif │ │ ├── nucex.gif │ │ ├── osi.gif │ │ └── pro_proex.gif │ │ ├── mummer-help.gif │ │ └── mummer-users.gif ├── scripts │ ├── Foundation.pm │ ├── Makefile │ ├── dnadiff.pl │ ├── exact-tandems.csh │ ├── mapview.pl │ ├── mummerplot.pl │ ├── nucmer.pl │ ├── nucmer2xfig.pl │ ├── promer.pl │ ├── run-mummer1.csh │ ├── run-mummer3.csh │ └── tandem-repeat.awk └── src │ ├── kurtz │ ├── Makedef │ ├── Makefile │ ├── README │ ├── Splintoptions │ ├── libbasedir │ │ ├── Cuthere.awk │ │ ├── Dependencies.mf │ │ ├── Excludemulti │ │ ├── Filegoals.mf │ │ ├── Filelists.mf │ │ ├── Importfiles │ │ ├── Makefile │ │ ├── Mkprotodef.sh │ │ ├── Mksrc.sh │ │ ├── README │ │ ├── args.h │ │ ├── arraydef.h │ │ ├── chardef.h │ │ ├── cleanMUMcand.c │ │ ├── clock.c │ │ ├── debug.c │ │ ├── debugdef.h │ │ ├── errordef.h │ │ ├── fopen.h │ │ ├── intbits.h │ │ ├── mapfile.c │ │ ├── megabytes.h │ │ ├── minmax.h │ │ ├── multidef.h │ │ ├── multiseq.c │ │ ├── mumcand.h │ │ ├── optdesc.h │ │ ├── procopt.c │ │ ├── protodef.h │ │ ├── safescpy.c │ │ ├── seterror.c │ │ ├── space.c │ │ ├── spacedef.h │ │ ├── types.h │ │ └── visible.h │ ├── mm3src │ │ ├── Dependencies.mf │ │ ├── Filegoals.mf │ │ ├── Makefile │ │ ├── README │ │ ├── findmaxmat.c │ │ ├── findmumcand.c │ │ ├── maxmat3.c │ │ ├── maxmatdef.h │ │ ├── maxmatinp.c │ │ ├── maxmatopt.c │ │ └── procmaxmat.c │ └── streesrc │ │ ├── Dependencies.mf │ │ ├── Filegoals.mf │ │ ├── Macronames │ │ ├── Makefile │ │ ├── Mkstreeproto.sh │ │ ├── access.c │ │ ├── addleafcount.c │ │ ├── construct.c │ │ ├── construct.gen │ │ ├── depthtab.c │ │ ├── dfs.c │ │ ├── dfs.gen │ │ ├── ex2leav.c │ │ ├── iterator.c │ │ ├── linkloc.c │ │ ├── loc.c │ │ ├── overmax.c │ │ ├── oversucc.c │ │ ├── scanpref.c │ │ ├── stree.c │ │ ├── streeacc.h │ │ ├── streedbg.c │ │ ├── streedef.h │ │ ├── streefiledoc.c │ │ ├── streehuge.h │ │ ├── streelarge.h │ │ ├── streemac.h │ │ ├── streeproto.h │ │ ├── streesmall.h │ │ ├── streetyp.h │ │ └── symboldef.h │ └── tigr │ ├── Makefile │ ├── annotate.cc │ ├── combineMUMs.cc │ ├── 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