mummer_3.23+dfsg-4_i386.deb


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Description

mummer - Efficient sequence alignment of full genomes

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename mummer_3.23+dfsg-4_i386.deb
Package name mummer
Package version 3.23+dfsg
Package release 4
Package architecture i386
Package type deb
Category field::biology field::biology:bioinformatics implemented-in::c++ interface::commandline role::program science scope::utility use::comparing works-with-format::TODO works-with-format::plaintext works-with::TODO
Homepage http://mummer.sourceforge.net/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 793.91 KB
Installed size 1.85 MB
MUMmer is a system for rapidly aligning entire genomes, whether
in complete or draft form. For example, MUMmer 3.0 can find all
20-basepair or longer exact matches between a pair of 5-megabase genomes
in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop
computer. 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. If the species are too divergent for
DNA sequence alignment to detect similarity, then the PROmer program
can generate alignments based upon the six-frame translations of both
input sequences.

Alternatives

Package Version Architecture Repository
mummer_3.23+dfsg-4_amd64.deb 3.23+dfsg amd64 Debian Main
mummer - - -

Requires

Name Value
gawk -
libc6 >= 2.7
libgcc1 >= 1:3.0
libstdc++6 >= 5.2
perl -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package mummer_3.23+dfsg-4_i386.deb
Source Package mummer

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install mummer deb package:
    # sudo apt-get install mummer

Files

Path
/usr/bin/combineMUMs
/usr/bin/delta-filter
/usr/bin/delta2blocks
/usr/bin/delta2maf
/usr/bin/dnadiff
/usr/bin/exact-tandems
/usr/bin/gaps
/usr/bin/mapview
/usr/bin/mgaps
/usr/bin/mummer
/usr/bin/mummer-annotate
/usr/bin/mummerplot
/usr/bin/nucmer
/usr/bin/nucmer2xfig
/usr/bin/promer
/usr/bin/repeat-match
/usr/bin/run-mummer1
/usr/bin/run-mummer3
/usr/bin/show-aligns
/usr/bin/show-coords
/usr/bin/show-diff
/usr/bin/show-snps
/usr/bin/show-tiling
/usr/lib/mummer/postnuc
/usr/lib/mummer/postpro
/usr/lib/mummer/prenuc
/usr/lib/mummer/prepro
/usr/lib/mummer/tandem-repeat.awk
/usr/share/doc/mummer/ACKNOWLEDGEMENTS
/usr/share/doc/mummer/NEWS.Debian.gz
/usr/share/doc/mummer/README.Debian
/usr/share/doc/mummer/README.gz
/usr/share/doc/mummer/changelog.Debian.gz
/usr/share/doc/mummer/changelog.gz
/usr/share/doc/mummer/copyright
/usr/share/doc/mummer/examples/expected/mapview_0.fig.gz
/usr/share/doc/mummer/examples/expected/mummer.mums.gz
/usr/share/doc/mummer/examples/expected/mummer3.align.gz
/usr/share/doc/mummer/examples/expected/mummer3.errorsgaps.gz
/usr/share/doc/mummer/examples/expected/mummer3.gaps.gz
/usr/share/doc/mummer/examples/expected/mummer3.out.gz
/usr/share/doc/mummer/examples/expected/nucmer.coords.gz
/usr/share/doc/mummer/examples/expected/nucmer.delta
/usr/share/doc/mummer/examples/expected/nucmer.snps.gz
/usr/share/doc/mummer/examples/expected/nucmer.tiling
/usr/share/doc/mummer/examples/expected/promer.aligns
/usr/share/doc/mummer/examples/expected/promer.coords.gz
/usr/share/doc/mummer/examples/expected/promer.delta.gz
/usr/share/doc/mummer/examples/input/B_anthracis_Mslice.fasta.gz
/usr/share/doc/mummer/examples/input/B_anthracis_contigs.fasta.gz
/usr/share/doc/mummer/examples/input/D_melanogaster_2Rslice.cds
/usr/share/doc/mummer/examples/input/D_melanogaster_2Rslice.fasta.gz
/usr/share/doc/mummer/examples/input/D_melanogaster_2Rslice.utr
/usr/share/doc/mummer/examples/input/D_pseudoobscura_contigs.fasta.gz
/usr/share/doc/mummer/examples/input/H_pylori26695_Bslice.fasta.gz
/usr/share/doc/mummer/examples/input/H_pylori26695_Eslice.fasta.gz
/usr/share/doc/mummer/examples/input/H_pyloriJ99_Bslice.fasta.gz
/usr/share/doc/mummer/examples/input/H_pyloriJ99_Eslice.fasta.gz
/usr/share/man/man1/combineMUMs.1.gz
/usr/share/man/man1/delta-filter.1.gz
/usr/share/man/man1/delta2blocks.1.gz
/usr/share/man/man1/delta2maf.1.gz
/usr/share/man/man1/dnadiff.1.gz
/usr/share/man/man1/exact-tandems.1.gz
/usr/share/man/man1/gaps.1.gz
/usr/share/man/man1/mapview.1.gz
/usr/share/man/man1/mgaps.1.gz
/usr/share/man/man1/mummer-annotate.1.gz
/usr/share/man/man1/mummer.1.gz
/usr/share/man/man1/mummerplot.1.gz
/usr/share/man/man1/nucmer.1.gz
/usr/share/man/man1/nucmer2xfig.1.gz
/usr/share/man/man1/promer.1.gz
/usr/share/man/man1/repeat-match.1.gz
/usr/share/man/man1/run-mummer1.1.gz
/usr/share/man/man1/run-mummer3.1.gz
/usr/share/man/man1/show-aligns.1.gz
/usr/share/man/man1/show-coords.1.gz
/usr/share/man/man1/show-diff.1.gz
/usr/share/man/man1/show-snps.1.gz
/usr/share/man/man1/show-tiling.1.gz
/usr/share/perl5/Foundation.pm

Changelog

2018-06-11 - Andreas Tille <tille@debian.org>
mummer (3.23+dfsg-4) unstable; urgency=medium
[ Helmut Grohne ]
* Fix FTCBFS: Let dh_auto_build pass cross tools to make. (Closes: #901261)
[ Andreas Tille ]
* Standards-Version: 4.1.4
* Point Vcs-fields to Salsa
* debhelper 11
* doc-base: debhelper 11 moves docs to /usr/share/doc/mummer - adapt path
2018-02-11 - Afif Elghraoui <afif@debian.org>
mummer (3.23+dfsg-3) unstable; urgency=low
* Team upload
[ Fabian Klötzl ]
* improve performance of delta2maf
[ Steffen Moeller ]
* Corrected EDAM annotation file
[ Afif Elghraoui ]
* d/watch: point to new upstream repository at GitHub
[ Andreas Tille ]
* Update d/copyright
2016-11-17 - Andreas Tille <tille@debian.org>
mummer (3.23+dfsg-2) unstable; urgency=medium
* Deactivate broken patch from mugsy that was taken over in last Debian
release
Closes: #843621
* debhelper 10
* d/watch: version=4
2016-07-24 - Canberk Koç <canberkkoc@gmail.com>
mummer (3.23+dfsg-1) unstable; urgency=medium
* Team upload
[ Andreas Tille ]
* Moved packaging from SVN to Git
* d/copyright: use Files-Excluded to clean up upstream source
* cme fix dpkg-control
* fix more spelling issues
* hardening=+all
[ Canberk Koç ]
* Autopkgtest added
2015-04-13 - Andreas Tille <tille@debian.org>
mummer (3.23~dfsg-3) unstable; urgency=medium
* Moved debian/upstream to debian/upstream/metadata
* Add some patches from mugsy enhancing functionality by adding two tools
* Add some patches from mugsy to include delta-filter -b for reporting
duplications
* cme fix dpkg-control
* Remove SF privacy breach script from docs
* Fix manpage syntax and add missing manpage
* Propagate hardening options
2012-04-21 - Andreas Tille <tille@debian.org>
mummer (3.23~dfsg-2) unstable; urgency=low
* debian/enable_building_with_tetex.patch: enable building with recent
tetex by changing the layout slightly (s/a4wide/a4/)
Closes: #669521
* debian/control: Standards-Version: 3.9.3 (no changes needed)
* Debhelper 9 (control+compat)
2012-02-07 - Charles Plessy <plessy@debian.org>
mummer (3.23~dfsg-1) unstable; urgency=low
* New upstream release adding -D and --banded option to nucmer.
* Updated debian/patches/02at_docs_web.diff.
* Corrected VCS URLs (debian/control).
* Conforms to Policy 3.9.2 (debian/control, no other changes needed).
* Using Debhelper 8 (debian/control, debian/compat).
* Support DEB_BUILD_OPTIONS via Debhelper (debian/rules).
* Use dpkg source format 3.0 (quilt) as a patch system (debian/rules,
debian/control, debian/source/format).
* Simplify debian/rules using dh.
* Pass Dpkg build flags in CFLAGS (debian/rules).
2010-03-24 - Andreas Tille <tille@debian.org>
mummer (3.22~dfsg-2) unstable; urgency=low
[ Andreas Tille ]
* Make sure scripts will use the installation path instead of
the temporary build path
Closes: #575105
* Make real use of debian/sh-replacement-scripts and drop csh
(build-)dependency
* incremented Standards-Version to reflect concordance with Debian Policy
3.8.4 (no changes needed).
* install tandem-repeat.awk which was lacking from installation
previousely
[ Charles Plessy ]
* Updated upstream-metadata.yaml to use simple key=value form
instead of BibTeX entry

See Also

Package Description
mumps-test_5.1.2-4+b2_i386.deb Example/test binaries using MUMPS
mumudvb_1.7.1-1+b1_i386.deb multicasts all channels of a DVB transponder on a network
munge_0.5.13-2_i386.deb authentication service to create and validate credentials
munin-async_2.0.49-1_all.deb network-wide graphing framework (async master/client)
munin-common_2.0.49-1_all.deb network-wide graphing framework (common)
munin-doc_2.0.49-1_all.deb network-wide graphing framework (documentation)
munin-libvirt-plugins_0.0.6-1_all.deb Munin plugins using libvirt
munin-node-c_0.0.13-1_i386.deb C rewrite of Munin node
munin-node_2.0.49-1_all.deb network-wide graphing framework (node)
munin-plugins-btrfs_11-2_all.deb munin plugin for monitoring btrfs filesystems
munin-plugins-c_0.0.13-1_i386.deb C rewrite of some Munin plugins
munin-plugins-core_2.0.49-1_all.deb network-wide graphing framework (plugins for node)
munin-plugins-extra_2.0.49-1_all.deb network-wide graphing framework (user contributed plugins for node)
munin-plugins-java_2.0.49-1_all.deb network-wide graphing framework (java plugins for node)
munin_2.0.49-1_all.deb network-wide graphing framework (grapher/gatherer)
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