last-align_490-1_amd64.deb


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Description

last-align - genome-scale comparison of biological sequences

Distribution: Debian 8 (Jessie)
Repository: Debian Main amd64
Package name: last-align
Package version: 490
Package release: 1
Package architecture: amd64
Package type: deb
Installed size: 1.26 KB
Download size: 447.27 KB
Official Mirror: ftp.br.debian.org
LAST is software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. Here are two things LAST is good at: * Comparing large (e.g. mammalian) genomes. * Mapping lots of sequence tags onto a genome. The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed size (e.g. BLAST uses 10-mers). This allows one to map tags to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. To find these variable-sized matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a discontiguous suffix array, analogous to spaced seeds.

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    Download

    Source package: last-align

    Install Howto

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

    Files

    • /usr/bin/last-dotplot
    • /usr/bin/last-map-probs
    • /usr/bin/last-merge-batches
    • /usr/bin/last-pair-probs
    • /usr/bin/last-postmask
    • /usr/bin/last-split
    • /usr/bin/lastal
    • /usr/bin/lastdb
    • /usr/bin/lastex
    • /usr/bin/maf-convert
    • /usr/bin/maf-cull
    • /usr/bin/maf-join
    • /usr/bin/maf-sort
    • /usr/bin/maf-swap
    • /usr/bin/parallel-fasta
    • /usr/bin/parallel-fastq
    • /usr/share/doc-base/last-align-lastex
    • /usr/share/doc-base/last-align-manual
    • /usr/share/doc-base/last-align-scripts
    • /usr/share/doc-base/last-align-seeds
    • /usr/share/doc/last-align/FAQ.html
    • /usr/share/doc/last-align/FAQ.txt
    • /usr/share/doc/last-align/Makefile
    • /usr/share/doc/last-align/NEWS.Debian.gz
    • /usr/share/doc/last-align/bisulfite.html
    • /usr/share/doc/last-align/bisulfite.txt
    • /usr/share/doc/last-align/changelog.Debian.gz
    • /usr/share/doc/last-align/changelog.gz
    • /usr/share/doc/last-align/copyright
    • /usr/share/doc/last-align/last-doc.css
    • /usr/share/doc/last-align/last-map-probs.html
    • /usr/share/doc/last-align/last-map-probs.txt
    • /usr/share/doc/last-align/last-pair-probs.html
    • /usr/share/doc/last-align/last-pair-probs.txt.gz
    • /usr/share/doc/last-align/last-postmask.html
    • /usr/share/doc/last-align/last-postmask.txt
    • /usr/share/doc/last-align/last-scripts.txt
    • /usr/share/doc/last-align/last-split.html
    • /usr/share/doc/last-align/last-split.txt.gz
    • /usr/share/doc/last-align/last-tutorial.html
    • /usr/share/doc/last-align/last-tutorial.txt.gz
    • /usr/share/doc/last-align/last.html
    • /usr/share/doc/last-align/last.txt.gz
    • /usr/share/doc/last-align/lastal.txt.gz
    • /usr/share/doc/last-align/lastdb.txt.gz
    • /usr/share/doc/last-align/lastex.txt.gz
    • /usr/share/doc/last-align/maf-convert.html
    • /usr/share/doc/last-align/maf-convert.txt
    • /usr/share/doc/last-align/maf-cull.html
    • /usr/share/doc/last-align/maf-cull.txt
    • /usr/share/doc/last-align/tag-seeds.txt.gz
    • /usr/share/doc/last-align/examples/chickenMito.fa.gz
    • /usr/share/doc/last-align/examples/fuguMito.fa.gz
    • /usr/share/doc/last-align/examples/hoxd70.mat
    • /usr/share/doc/last-align/examples/humanMito.fa.gz
    • /usr/share/doc/last-align/examples/last-bisulfite-paired.sh
    • /usr/share/doc/last-align/examples/last-bisulfite.sh
    • /usr/share/doc/last-align/examples/mouseMito.fa.gz
    • /usr/share/doc/last-align/examples/multiMito.maf.gz
    • /usr/share/doc/last-align/examples/multiMito.sh
    • /usr/share/doc/last-align/examples/myalns.maf.gz
    • /usr/share/doc/last-align/examples/titv212.mat
    • /usr/share/doc/last-align/examples/vertebrateMito.gc
    • /usr/share/doc/last-align/examples/yass.seed
    • /usr/share/man/man1/last-dotplot.1.gz
    • /usr/share/man/man1/last-map-probs.1.gz
    • /usr/share/man/man1/last-pair-probs.1.gz
    • /usr/share/man/man1/last-split.1.gz
    • /usr/share/man/man1/lastal.1.gz
    • /usr/share/man/man1/lastdb.1.gz
    • /usr/share/man/man1/lastex.1.gz
    • /usr/share/man/man1/maf-convert.1.gz
    • /usr/share/man/man1/maf-cull.1.gz
    • /usr/share/man/man1/maf-join.1.gz
    • /usr/share/man/man1/maf-sort.1.gz
    • /usr/share/man/man1/maf-swap.1.gz

    Changelog

    2014-10-23 - Andreas Tille <tille@debian.org> last-align (490-1) unstable; urgency=medium * New upstream version * get-orig-source target now with xz compression * cme fix dpkg-control * Upstream dropped .py suffix - adpapt help2man calls in d/rules

    2014-08-16 - Charles Plessy <plessy@debian.org> last-align (475-1) unstable; urgency=medium * New upstream release. * debian/rules: - removed compression command, as it is now the default. - removed manual page of last-merge-batches.py. * debian/control: suggest GNU parallel. * debian/README.source: removed as conversion from zip is now automagic.

    2014-03-21 - Andreas Tille <tille@debian.org> last-align (418-1) unstable; urgency=medium * New upstream release * debian/upstream -> debian/upstream/metadata

    2014-01-28 - Andreas Tille <tille@debian.org> last-align (393-1) unstable; urgency=medium * New upstream release * cme fix dpkg-control * debian/rules: Adapt help2man to the fact that two scripts were deleted from upstream source (no idea how to write manpages for the new parallel-* scripts) * Adapt doc-base control script (text file might be uncompressed)

    2013-10-06 - Charles Plessy <plessy@debian.org> last-align (359-1) unstable; urgency=low * New upstream release. * debian/control: - Removed Pre-Depends on dpkg as Ubuntu LTS is released. - Removed obsolete DM-Upload-Allowed field. - Use canonical VCS URLs. - Normalised with config-model-edit. - Removed version constraint on help2man, satisfied in oldstable. - Mark conformance with Policy version 3.9.4. * debian/watch: updated. * debian/rules: - Restore xz compression of the binary packages. - Produce a manual page for ‘last-split’ with help2man.

    2012-05-07 - Andreas Tille <tille@debian.org> last-align (199-1) unstable; urgency=low [ Charles Plessy ] * Summarise LAST license in debian/copyright header. [ Andreas Tille ] * New upstream version Closes: #667939 * debian/rules: - switch from cdbs to dh - add help2man call for lastex * debian/install: - removed to use upstream install target (which also installs lastex) * debian/copyright: Make Source field more generic

    2012-04-02 - Andreas Tille <tille@debian.org> last-align (198-1) unstable; urgency=low * New upstream version * debian/rules,debian/get-orig-source: Simplified downloading original source * debhelper 9 to enable hardening flags (control+compat, closes: #667939).

    2012-03-08 - Andreas Tille <tille@debian.org> last-align (193-1) unstable; urgency=low * New upstream version * debian/upstream: Removed duplicate entries for DOI/PMID * debian/control: Standards-Version: 3.9.3 (no changes needed)

    2011-10-22 - Charles Plessy <plessy@debian.org> last-align (189-1) unstable; urgency=low * New upstream release. * Autogenerate a manual page for last-merge-batches (debian/rules).

    2011-10-17 - Colin Watson <cjwatson@ubuntu.com> last-align (184-1ubuntu1) precise; urgency=low * Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until after Ubuntu 12.04 LTS.

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