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locks; strict; comment @# @; 1.7 date 2009.06.14.17.34.34; author joerg; state Exp; branches; next 1.6; 1.6 date 2008.10.11.22.01.13; author schwarz; state Exp; branches; next 1.5; 1.5 date 2007.01.18.19.13.10; author rillig; state Exp; branches; next 1.4; 1.4 date 2006.06.21.19.01.12; author minskim; state Exp; branches; next 1.3; 1.3 date 2006.01.29.19.31.43; author schwarz; state Exp; branches; next 1.2; 1.2 date 2004.12.05.15.24.54; author cube; state Exp; branches; next 1.1; 1.1 date 2003.09.27.22.24.57; author jschauma; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2003.09.27.22.24.57; author jschauma; state Exp; branches; next ; desc @@ 1.7 log @Remove @@dirrm entries from PLISTs @ text @@@comment $NetBSD: PLIST,v 1.6 2008/10/11 22:01:13 schwarz Exp $ bin/annotate bin/combineMUMs bin/delta-filter 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-snps bin/show-tiling share/doc/mummer/README share/doc/mummer/differences.README share/doc/mummer/dnadiff.README share/doc/mummer/mapview.README 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/doc/mummer/web/MUMmer.pdf share/doc/mummer/web/MUMmer2.pdf share/doc/mummer/web/MUMmer3.pdf share/doc/mummer/web/XFiles.pdf share/doc/mummer/web/applications.html share/doc/mummer/web/compare.html share/doc/mummer/web/examples/data/B_anthracis_Mslice.fasta share/doc/mummer/web/examples/data/B_anthracis_contigs.fasta share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.cds share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.fasta share/doc/mummer/web/examples/data/D_melanogaster_2Rslice.utr share/doc/mummer/web/examples/data/D_pseudoobscura_contigs.fasta share/doc/mummer/web/examples/data/H_pylori26695_Bslice.fasta share/doc/mummer/web/examples/data/H_pylori26695_Eslice.fasta share/doc/mummer/web/examples/data/H_pyloriJ99_Bslice.fasta share/doc/mummer/web/examples/data/H_pyloriJ99_Eslice.fasta share/doc/mummer/web/examples/data/README share/doc/mummer/web/examples/data/mapview_0.fig share/doc/mummer/web/examples/data/mapview_0.pdf share/doc/mummer/web/examples/data/mummer.fplot share/doc/mummer/web/examples/data/mummer.gp share/doc/mummer/web/examples/data/mummer.mums share/doc/mummer/web/examples/data/mummer.ps share/doc/mummer/web/examples/data/mummer.rplot share/doc/mummer/web/examples/data/mummer1.align share/doc/mummer/web/examples/data/mummer1.errorsgaps share/doc/mummer/web/examples/data/mummer1.gaps share/doc/mummer/web/examples/data/mummer1.out share/doc/mummer/web/examples/data/mummer3.align share/doc/mummer/web/examples/data/mummer3.errorsgaps share/doc/mummer/web/examples/data/mummer3.gaps share/doc/mummer/web/examples/data/mummer3.out share/doc/mummer/web/examples/data/nucmer.cluster share/doc/mummer/web/examples/data/nucmer.coords share/doc/mummer/web/examples/data/nucmer.delta share/doc/mummer/web/examples/data/nucmer.snps share/doc/mummer/web/examples/data/nucmer.tiling share/doc/mummer/web/examples/data/promer.aligns share/doc/mummer/web/examples/data/promer.cluster share/doc/mummer/web/examples/data/promer.coords share/doc/mummer/web/examples/data/promer.delta share/doc/mummer/web/examples/dotplot.gif share/doc/mummer/web/examples/examples_logo.gif share/doc/mummer/web/examples/index.html share/doc/mummer/web/examples/mapplot.gif share/doc/mummer/web/examples/mapview_fig.jpg share/doc/mummer/web/examples/mummer_ps.jpg share/doc/mummer/web/index.html share/doc/mummer/web/logo.gif share/doc/mummer/web/manual/AlignmentTypes.odg share/doc/mummer/web/manual/AlignmentTypes.pdf share/doc/mummer/web/manual/covplot.gif share/doc/mummer/web/manual/dotplot.gif share/doc/mummer/web/manual/gaps.gif share/doc/mummer/web/manual/index.html share/doc/mummer/web/manual/manual_logo.gif share/doc/mummer/web/manual/mapplot.gif share/doc/mummer/web/manual/mgaps.gif share/doc/mummer/web/manual/multiplota.gif share/doc/mummer/web/manual/multiplotb.gif share/doc/mummer/web/manual/nuc_proex.gif share/doc/mummer/web/manual/nucex.gif share/doc/mummer/web/manual/osi.gif share/doc/mummer/web/manual/pro_proex.gif share/doc/mummer/web/mummer-help.gif share/doc/mummer/web/mummer-users.gif share/mummer/dnadiff share/mummer/exact-tandems share/mummer/mapview share/mummer/mummerplot share/mummer/nucmer share/mummer/nucmer2xfig share/mummer/promer share/mummer/run-mummer1 share/mummer/run-mummer3 @ 1.6 log @updated to MUMmer3.20 @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.5 2007/01/18 19:13:10 rillig Exp $ a103 6 @@dirrm share/mummer @@dirrm share/doc/mummer/web/manual @@dirrm share/doc/mummer/web/examples/data @@dirrm share/doc/mummer/web/examples @@dirrm share/doc/mummer/web @@dirrm share/doc/mummer @ 1.5 log @Updated mummer to 3.19. Changes since 3.18: - More documentation. @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.4 2006/06/21 19:01:12 minskim Exp $ d19 1 d95 1 @ 1.4 log @Reorder dirrm@@'s so that the package is deinstalled propertly. PKGREVISION will be bumped with another change shortly. @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.3 2006/01/29 19:31:43 schwarz Exp $ d17 2 a18 63 share/doc/html/mummer/MUMmer.pdf share/doc/html/mummer/MUMmer2.pdf share/doc/html/mummer/MUMmer3.pdf share/doc/html/mummer/XFiles.pdf share/doc/html/mummer/applications.html share/doc/html/mummer/compare.html share/doc/html/mummer/index.html share/doc/html/mummer/logo.gif share/doc/html/mummer/mummer-help.gif share/doc/html/mummer/mummer-users.gif share/doc/html/mummer/examples/dotplot.gif share/doc/html/mummer/examples/examples_logo.gif share/doc/html/mummer/examples/index.html share/doc/html/mummer/examples/mapplot.gif share/doc/html/mummer/examples/mapview_fig.jpg share/doc/html/mummer/examples/mummer_ps.jpg share/doc/html/mummer/examples/data/B_anthracis_Mslice.fasta share/doc/html/mummer/examples/data/B_anthracis_contigs.fasta share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.cds share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.fasta share/doc/html/mummer/examples/data/D_melanogaster_2Rslice.utr share/doc/html/mummer/examples/data/D_pseudoobscura_contigs.fasta share/doc/html/mummer/examples/data/H_pylori26695_Bslice.fasta share/doc/html/mummer/examples/data/H_pylori26695_Eslice.fasta share/doc/html/mummer/examples/data/H_pyloriJ99_Bslice.fasta share/doc/html/mummer/examples/data/H_pyloriJ99_Eslice.fasta share/doc/html/mummer/examples/data/README share/doc/html/mummer/examples/data/mapview_0.fig share/doc/html/mummer/examples/data/mapview_0.pdf share/doc/html/mummer/examples/data/mummer.fplot share/doc/html/mummer/examples/data/mummer.gp share/doc/html/mummer/examples/data/mummer.mums share/doc/html/mummer/examples/data/mummer.ps share/doc/html/mummer/examples/data/mummer.rplot share/doc/html/mummer/examples/data/mummer1.align share/doc/html/mummer/examples/data/mummer1.errorsgaps share/doc/html/mummer/examples/data/mummer1.gaps share/doc/html/mummer/examples/data/mummer1.out share/doc/html/mummer/examples/data/mummer3.align share/doc/html/mummer/examples/data/mummer3.errorsgaps share/doc/html/mummer/examples/data/mummer3.gaps share/doc/html/mummer/examples/data/mummer3.out share/doc/html/mummer/examples/data/nucmer.cluster share/doc/html/mummer/examples/data/nucmer.coords share/doc/html/mummer/examples/data/nucmer.delta share/doc/html/mummer/examples/data/nucmer.snps share/doc/html/mummer/examples/data/nucmer.tiling share/doc/html/mummer/examples/data/promer.aligns share/doc/html/mummer/examples/data/promer.cluster share/doc/html/mummer/examples/data/promer.coords share/doc/html/mummer/examples/data/promer.delta share/doc/html/mummer/manual/covplot.gif share/doc/html/mummer/manual/dotplot.gif share/doc/html/mummer/manual/gaps.gif share/doc/html/mummer/manual/index.html share/doc/html/mummer/manual/manual_logo.gif share/doc/html/mummer/manual/mgaps.gif share/doc/html/mummer/manual/multiplota.gif share/doc/html/mummer/manual/multiplotb.gif share/doc/html/mummer/manual/nuc_proex.gif share/doc/html/mummer/manual/nucex.gif share/doc/html/mummer/manual/osi.gif share/doc/html/mummer/manual/pro_proex.gif d28 66 d103 4 a107 4 @@dirrm share/doc/html/mummer/examples/data @@dirrm share/doc/html/mummer/examples @@dirrm share/doc/html/mummer/manual @@dirrm share/doc/html/mummer @ 1.3 log @ Updated biology/mummer to release 3.18. Changes include: - MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.2 2004/12/05 15:24:54 cube Exp $ d99 3 a102 3 @@dirrm share/doc/html/mummer/manual @@dirrm share/doc/html/mummer/examples @@dirrm share/doc/html/mummer/examples/data @ 1.2 log @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. @ text @d1 1 a1 1 @@comment $NetBSD$ d4 1 d15 1 d17 6 a22 4 share/doc/html/mummer/covplot.gif share/doc/html/mummer/dotplot.gif share/doc/html/mummer/email.jpg share/doc/html/mummer/gaps.gif d24 57 a80 6 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 d90 1 d100 3 @ 1.1 log @Initial revision @ text @a25 1 share/doc/mummer/maxmat3man.pdf @ 1.1.1.1 log @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. @ text @@