exonerate_2.4.0-4_i386.deb


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Description

exonerate - generic tool for pairwise sequence comparison

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename exonerate_2.4.0-4_i386.deb
Package name exonerate
Package version 2.4.0
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::TODO use::searching works-with-format::TODO works-with-format::plaintext works-with::TODO
Homepage https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 1.61 MB
Installed size 8.68 MB
Exonerate allows you to align sequences using a many alignment models, using
either exhaustive dynamic programming, or a variety of heuristics. Much of
the functionality of the Wise dynamic programming suite was reimplemented in C
for better efficiency. Exonerate is an intrinsic component of the building of
the Ensembl genome databases, providing similarity scores between RNA and DNA
sequences and thus determining splice variants and coding sequences in
general.
An In-silico PCR Experiment Simulation System (see the ipcress man page) is
packaged with exonerate.
This package also comes with a selection of utilities for performing
simple manipulations quickly on fasta files beyond 2Gb

Alternatives

Package Version Architecture Repository
exonerate_2.4.0-4_amd64.deb 2.4.0 amd64 Debian Main
exonerate - - -

Requires

Name Value
libc6 >= 2.7
libglib2.0-0 >= 2.24.0

Download

Type URL
Mirror ftp.br.debian.org
Binary Package exonerate_2.4.0-4_i386.deb
Source Package exonerate

Install Howto

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

Files

Path
/usr/bin/esd2esi
/usr/bin/exonerate
/usr/bin/exonerate-server
/usr/bin/fasta2esd
/usr/bin/fastaannotatecdna
/usr/bin/fastachecksum
/usr/bin/fastaclean
/usr/bin/fastaclip
/usr/bin/fastacomposition
/usr/bin/fastadiff
/usr/bin/fastaexplode
/usr/bin/fastafetch
/usr/bin/fastahardmask
/usr/bin/fastaindex
/usr/bin/fastalength
/usr/bin/fastanrdb
/usr/bin/fastaoverlap
/usr/bin/fastareformat
/usr/bin/fastaremove
/usr/bin/fastarevcomp
/usr/bin/fastasoftmask
/usr/bin/fastasort
/usr/bin/fastasplit
/usr/bin/fastasubseq
/usr/bin/fastatranslate
/usr/bin/fastavalidcds
/usr/bin/ipcress
/usr/share/doc/exonerate/AUTHORS
/usr/share/doc/exonerate/ChangeLog.gz
/usr/share/doc/exonerate/README.gz
/usr/share/doc/exonerate/TODO.gz
/usr/share/doc/exonerate/changelog.Debian.gz
/usr/share/doc/exonerate/changelog.gz
/usr/share/doc/exonerate/copyright
/usr/share/doc/exonerate/examples/data/cdna/calm.human.dna.fasta
/usr/share/doc/exonerate/examples/data/cdna/htrt.human.dna.fasta.gz
/usr/share/doc/exonerate/examples/data/cdna/p53.human.dna.fasta
/usr/share/doc/exonerate/examples/data/cdna/tube.drome.dna.fasta
/usr/share/doc/exonerate/examples/data/protein/calm.human.protein.fasta
/usr/share/doc/exonerate/examples/data/protein/htrt.human.protein.fasta
/usr/share/doc/exonerate/examples/data/protein/p53.human.protein.fasta
/usr/share/doc/exonerate/examples/data/protein/tube.drome.protein.fasta
/usr/share/doc/exonerate/examples/exonerate/exonerate.simple.test.sh
/usr/share/doc/exonerate/examples/ipcress/ipcress.simple.test.sh
/usr/share/doc/exonerate/examples/util/fastaclean.test.sh
/usr/share/doc/exonerate/examples/util/fastaclip.test.sh
/usr/share/doc/exonerate/examples/util/fastacomposition.test.sh
/usr/share/doc/exonerate/examples/util/fastadiff.test.sh
/usr/share/doc/exonerate/examples/util/fastaexpode.test.sh
/usr/share/doc/exonerate/examples/util/fastaindex.fastafetch.test.sh
/usr/share/doc/exonerate/examples/util/fastalength.test.sh
/usr/share/doc/exonerate/examples/util/fastanrdb.test.sh
/usr/share/doc/exonerate/examples/util/fastaoverlap.test.sh
/usr/share/doc/exonerate/examples/util/fastarefomat.test.sh
/usr/share/doc/exonerate/examples/util/fastaremove.test.sh
/usr/share/doc/exonerate/examples/util/fastarevcomp.test.sh
/usr/share/doc/exonerate/examples/util/fastasoftmask.fastahardmask.test.sh
/usr/share/doc/exonerate/examples/util/fastasort.test.sh
/usr/share/doc/exonerate/examples/util/fastasplit.test.sh
/usr/share/doc/exonerate/examples/util/fastasubseq.test.sh
/usr/share/doc/exonerate/examples/util/fastatranslate.test.sh
/usr/share/doc/exonerate/examples/util/fastavalidcds.test.sh
/usr/share/man/man1/esd2esi.1.gz
/usr/share/man/man1/exonerate-client.1.gz
/usr/share/man/man1/exonerate-server.1.gz
/usr/share/man/man1/exonerate.1.gz
/usr/share/man/man1/fasta2esd.1.gz
/usr/share/man/man1/fastaannotatecdna.1.gz
/usr/share/man/man1/fastachecksum.1.gz
/usr/share/man/man1/fastaclean.1.gz
/usr/share/man/man1/fastaclip.1.gz
/usr/share/man/man1/fastacomposition.1.gz
/usr/share/man/man1/fastadiff.1.gz
/usr/share/man/man1/fastaexplode.1.gz
/usr/share/man/man1/fastafetch.1.gz
/usr/share/man/man1/fastahardmask.1.gz
/usr/share/man/man1/fastaindex.1.gz
/usr/share/man/man1/fastalength.1.gz
/usr/share/man/man1/fastanrdb.1.gz
/usr/share/man/man1/fastaoverlap.1.gz
/usr/share/man/man1/fastareformat.1.gz
/usr/share/man/man1/fastaremove.1.gz
/usr/share/man/man1/fastarevcomp.1.gz
/usr/share/man/man1/fastasoftmask.1.gz
/usr/share/man/man1/fastasort.1.gz
/usr/share/man/man1/fastasplit.1.gz
/usr/share/man/man1/fastasubseq.1.gz
/usr/share/man/man1/fastatranslate.1.gz
/usr/share/man/man1/fastautils.1.gz
/usr/share/man/man1/fastavalidcds.1.gz
/usr/share/man/man1/ipcress.1.gz

Changelog

2019-01-06 - Andreas Tille <tille@debian.org>
exonerate (2.4.0-4) unstable; urgency=medium
[ Jelmer Vernooij ]
* Trim trailing whitespace.
* Use secure copyright file specification URI.
[ Andreas Tille ]
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.3.0
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
2018-01-23 - Andreas Tille <tille@debian.org>
exonerate (2.4.0-3) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata: Added references to registries.
[ Helmut Grohne ]
* make pkg-config macro cross compilation safe
Closes: #888032
[ Andreas Tille ]
* debhelper 11
* Standards-Version: 4.1.3
2016-05-18 - Canberk Koç <canberkkoc@gmail.com>
exonerate (2.4.0-2) unstable; urgency=medium
[ Canberk Koç ]
* Team upload
* debian/tests: added testsuite
* debian/rules: changes for testing
[ Andreas Tille ]
* cme fix dpkg-control
2016-03-20 - Andreas Tille <tille@debian.org>
exonerate (2.4.0-1) unstable; urgency=medium
* New upstream version
* Moved packaging from SVN to Git
* Better hardening
2016-01-11 - Andreas Tille <tille@debian.org>
exonerate (2.2.0-7) unstable; urgency=low
[ Charles Plessy ]
* renamed debian/upstream-metadata.yaml to debian/upstream/metadata
[ Andreas Tille ]
* debian/upstream/metadata:
- Took over some detail from tasks file; moved DOI+PMID
to References
- Added eprint
* debian/reference removed in favour of debian/upstream/metadata
* debian/copyright: Deleted bouncing upstream contact address
* fixed upstream homepage
* fix watch file
* do not maintain duplicated information in debian/upstream/metadata
* cme fix dpkg-control
* debhelper 9
* DEP5
* fix spelling and manpage syntax issues
* remove outdated README.Debian
2012-01-12 - Andreas Tille <tille@debian.org>
exonerate (2.2.0-6) unstable; urgency=low
* debian/patches/autoreconf.patch: Removed because not needed
when using dh-autoreconf
2012-01-12 - Andreas Tille <tille@debian.org>
exonerate (2.2.0-5) unstable; urgency=low
* Rather use dh-autoreconf as advised in another patch from
Micah Gersten <micahg@ubuntu.com> (thanks for your patience)
Finally Closes #651802
2012-01-06 - Andreas Tille <tille@debian.org>
exonerate (2.2.0-4) unstable; urgency=low
* Use autotools_dev properly
Closes: #651802
2011-12-12 - Andreas Tille <tille@debian.org>
exonerate (2.2.0-3) unstable; urgency=low
[ Charles Plessy ]
* Documented some meta-information in ‘debian/upstream-metadata.yaml’.
[ Andreas Tille ]
* debian/source/format: 3.0 (quilt)
* debian/control:
- Standards-Version: 3.9.2 (no changes needed)
- Fixed Vcs fields
* Debhlper 8 (control+compat)
* debian/copyright: some DEP5 changes
* debian/patches/fix_build-as-needed.patch: Fix build with --as-needed
(Thanks to Micah Gersten <micahg@ubuntu.com>)
Closes: #651802
* debian/patches/autoreconf.patch: Build with recent autotools
* debian/patches/manpages.patch: Fix some lintian warnings
* debian/rules:
- Convert to short dh notation
- Remove codegen in clean target
- Install upstream changelog only once
2009-09-13 - Andreas Tille <tille@debian.org>
exonerate (2.2.0-2) unstable; urgency=low
[ Charles Plessy ]
* debian/control:
- Enhances bioperl-run instead of bioperl.
- Incremented Standards-Version to reflect conformance with Policy
3.8.3 (no changes needed).
[ Andreas Tille ]
* debian/control
- s/libreadline5-dev/libreadline-dev/
- s/Debian-Med/Debian Med/

See Also

Package Description
expand-region-el_0.11.0-3_all.deb Transition package, expand-region-el to elpa-expand-region
expat_2.2.6-2_i386.deb XML parsing C library - example application
expect_5.45.4-2_i386.deb Automates interactive applications
expeyes-clib_4.4.4+dfsg-4_i386.deb hardware & software framework for developing science experiments
expeyes-doc-common_4.3-1_all.deb Common files related to the User manual for expeyes library
expeyes-doc-en_4.3-1_all.deb User manual for expeyes library, in English language
expeyes-doc-fr_4.3-1_all.deb User manual for expeyes library, French translation
expeyes-firmware-dev_4.4.4+dfsg-4_all.deb hardware & software framework for developing science experiments
expeyes-web_4.4.4+dfsg-4_all.deb Web interface for expEYES-Junior
expeyes_4.4.4+dfsg-4_all.deb hardware & software framework for developing science experiments
explain_1.4.D001-8_i386.deb utility to explain system call errors
ext3grep_0.10.2-4_i386.deb tool to help recover deleted files on ext3 filesystems
ext4magic_0.3.2-12_i386.deb recover deleted files from ext3 or ext4 partitions
extlinux_6.04~git20190206.bf6db5b4+dfsg1-1_i386.deb collection of bootloaders (Linux ext2/ext3/ext4, btrfs, and xfs bootloader)
extra-cmake-modules_5.54.0-1_i386.deb Extra modules and scripts for CMake
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