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Update to version 3.15. From David Price in PR#28305. 3.05 - Added -k option to show-coords to only display the best frame for overlapping PROmer alignments. Added --[no]optimize option to nucmer and promer to allow alignment score optimization to be turned off, i.e allow alignments to extend to the ends of sequences rather than backtracking to optimize the alignment score. Updated docs. 3.06 - Added -F and -h option to mummer. Changed -mumcand option to -mumreference, but left deprecated -mumcand option available. Added -maxmatch option to mummer, and changed default behavior of all applicable programs to -mumreference (nucmer, promer and mummer). Added -w (screen width) option to show-aligns. Updated documentation with all of these changes. 3.07 - Added the 'mapview' plotting utility and appropriate documentation. Fixed origin wrap shadowing bug in show-tiling when using the -c option. NUCmer and PROmer now convert to absolute paths to avoid ambiguity. 3.08 - Added MUMmer examples web docs which gives brief walkthroughs 3.10 - Now Mac OSX compatible. Added -R option to show-tiling. 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed the issue with mummerplot being to faint. 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed a bug in nucmer and promer. Fixed rounding issue in show-coords. Updated citations. 3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation. Fixed bug in show-tiling -R 3.14 - Fixed gcc3 compilation bug 3.15 - Fixed --nooptimize in nuc/promer.
2004-12-05 16:24:54 +01:00
@comment $NetBSD: PLIST,v 1.2 2004/12/05 15:24:54 cube Exp $
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
bin/annotate
bin/combineMUMs
bin/gaps
bin/mgaps
bin/mummer
bin/postnuc
bin/postpro
bin/prenuc
bin/prepro
bin/repeat-match
bin/show-aligns
bin/show-coords
bin/show-tiling
share/doc/html/mummer/covplot.gif
share/doc/html/mummer/dotplot.gif
share/doc/html/mummer/email.jpg
share/doc/html/mummer/gaps.gif
share/doc/html/mummer/index.html
share/doc/html/mummer/manual_logo.gif
share/doc/html/mummer/mgaps.gif
share/doc/html/mummer/nuc_proex.gif
share/doc/html/mummer/nucex.gif
share/doc/html/mummer/osi.gif
share/doc/html/mummer/pro_proex.gif
share/doc/mummer/maxmat3man.tex
share/doc/mummer/maxmat3src.pdf
share/doc/mummer/nucmer.README
share/doc/mummer/optionman.sty
share/doc/mummer/promer.README
share/doc/mummer/run-mummer1.README
share/doc/mummer/run-mummer3.README
share/doc/mummer/skaff.sty
share/mummer/exact-tandems
share/mummer/mummerplot
share/mummer/nucmer
share/mummer/nucmer2xfig
share/mummer/promer
share/mummer/run-mummer1
share/mummer/run-mummer3
@dirrm share/mummer
@dirrm share/doc/mummer
@dirrm share/doc/html/mummer
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