pynast_1.2.2-1_all.deb


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Description

pynast - alignment of short DNA sequences

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe amd64
Package name: pynast
Package version: 1.2.2
Package release: 1
Package architecture: all
Package type: deb
Installed size: 323 B
Download size: 74.80 KB
Official Mirror: archive.ubuntu.com
The package provices a reimplementation of the Nearest Alignment Space Termination tool in Python. It was prepared for next generation sequencers. Given a set of sequences and a template alignment, PyNAST will align the input sequences against the template alignment, and return a multiple sequence alignment which contains the same number of positions (or columns) as the template alignment. This facilitates the analysis of new sequences in the context of existing alignments, and additional data derived from existing alignments such as phylogenetic trees. Because any protein or nucleic acid sequences and template alignments can be provided, PyNAST is not limited to the analysis of 16s rDNA sequences.

Alternatives

Provides

  • python-pynast

Conflicts

  • python-pynast

Replaces

  • python-pynast

    Download

    Binary package: pynast_1.2.2-1_all.deb
    Source package: pynast

    Install Howto

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

    Files

    • /usr/bin/pynast
    • /usr/lib/python2.7/dist-packages/pynast-1.2.2.egg-info
    • /usr/lib/python2.7/dist-packages/pynast/__init__.py
    • /usr/lib/python2.7/dist-packages/pynast/logger.py
    • /usr/lib/python2.7/dist-packages/pynast/util.py
    • /usr/lib/python2.7/dist-packages/pynast/pycogent_backports/__init__.py
    • /usr/lib/python2.7/dist-packages/pynast/pycogent_backports/uclust.py
    • /usr/share/doc-base/pynast
    • /usr/share/doc/pynast/README.Debian
    • /usr/share/doc/pynast/README.md
    • /usr/share/doc/pynast/README.test
    • /usr/share/doc/pynast/changelog.Debian.gz
    • /usr/share/doc/pynast/copyright
    • /usr/share/doc/pynast/run-unit-test
    • /usr/share/doc/pynast/html/index.html
    • /usr/share/doc/pynast/html/install.html
    • /usr/share/doc/pynast/html/install_gui.html
    • /usr/share/doc/pynast/html/objects.inv
    • /usr/share/doc/pynast/html/search.html
    • /usr/share/doc/pynast/html/searchindex.js
    • /usr/share/doc/pynast/html/_sources/index.txt
    • /usr/share/doc/pynast/html/_sources/install.txt
    • /usr/share/doc/pynast/html/_sources/install_gui.txt
    • /usr/share/doc/pynast/html/_static/ajax-loader.gif
    • /usr/share/doc/pynast/html/_static/basic.css
    • /usr/share/doc/pynast/html/_static/comment-bright.png
    • /usr/share/doc/pynast/html/_static/comment-close.png
    • /usr/share/doc/pynast/html/_static/comment.png
    • /usr/share/doc/pynast/html/_static/default.css
    • /usr/share/doc/pynast/html/_static/doctools.js
    • /usr/share/doc/pynast/html/_static/down-pressed.png
    • /usr/share/doc/pynast/html/_static/down.png
    • /usr/share/doc/pynast/html/_static/file.png
    • /usr/share/doc/pynast/html/_static/jquery.js
    • /usr/share/doc/pynast/html/_static/minus.png
    • /usr/share/doc/pynast/html/_static/plus.png
    • /usr/share/doc/pynast/html/_static/pygments.css
    • /usr/share/doc/pynast/html/_static/searchtools.js
    • /usr/share/doc/pynast/html/_static/sidebar.js
    • /usr/share/doc/pynast/html/_static/underscore.js
    • /usr/share/doc/pynast/html/_static/up-pressed.png
    • /usr/share/doc/pynast/html/_static/up.png
    • /usr/share/doc/pynast/html/_static/websupport.js
    • /usr/share/doc/pynast/tests/all_tests.py
    • /usr/share/doc/pynast/tests/test_logger.py
    • /usr/share/doc/pynast/tests/test_util.py.gz
    • /usr/share/doc/pynast/tests/test_pycogent_backports/test_uclust.py.gz
    • /usr/share/man/man1/pynast.1.gz

    Changelog

    2014-08-11 - Andreas Tille <tille@debian.org> pynast (1.2.2-1) unstable; urgency=medium * New upsteam version now on Github (adapted d/watch) * debian/copyright: License change from GPL to BSD * rename source package from python-pynast to pynast * cme fix dpkg-control * debian/patches/do_not_install_privacy_breaching_scripts.patch: Do not install privacy breaking scripts * debian/rules: run unit tests * debian/control: - Build-Depends + Recommend packages needed in unit tests - Recommends: python-mpi4py * debian/patches/avoid_python-mpi4py_missing_warning.patch: Circumvent missing python-mpi4py at build time * Add autopkgtest

    2013-06-17 - Andreas Tille <tille@debian.org> python-pynast (1.2-1) unstable; urgency=low * Upload to Debian

    2013-06-11 - Tim Booth <tbooth@ceh.ac.uk> python-pynast (1.2-0biolinux1) precise; urgency=low * New upstream * New upstream location - changed watchfile

    2013-05-20 - Andreas Tille <tille@debian.org> python-pynast (1.1-4) unstable; urgency=low [ Charles Plessy ] * Renamed debian/upstream-metadata.yaml to debian/upstream. * Corrected VCS URLs (debian/control). [ Andreas Tille ] * debian/upstream: - Moved DOI/PMID to References section - Valid BibTeX authors field * debian/control: - Section: optional - Standards-Version: 3.9.4 (no changes needed) - Debhelper 9 (also in compat) - removed XS-Autobuild because package is in main - Drop Build-Depends: python-central Closes: #708889

    2011-11-29 - Andreas Tille <tille@debian.org> python-pynast (1.1-3) unstable; urgency=low [ Steffen Moeller ] * Rendering Tim's fixes available for Debian * Moving pynast from contrib to main. The dependency cogent got its non-freeness resolved. * Changing name from python-pynast to pynast. [ Andreas Tille ] * debian/control: - Added myself and Tim Booth <tbooth@ceh.ac.uk> to Uploaders - Fixed Vcs fields - Removed duplicated ${misc:Depends} - Removed unneeded ${shlibs:Depends} - Depends: libjs-jquery, libjs-underscore - Moved citation information from long description to upstream-metadata.yaml - Moved information about previous versions from long description to README.Debian - Provides/Replaces/Conflicts: python-pynast to enable smooth upgrades after renaming the package * debian/copyright: DEP5 * Dephelper 8 (control+compat) * debian/links: Link packages JavaScript libraries * debian/rules: remove incomplete links to JavaScript libraries * debian/doc-base: created docbase file * debian/pynast.1: escape hyphen character * debian/upstream-metadata.yaml: Citation information * debian/README.Debian: Replaced outdated and useless content by some information about previous upstream versions (previosely mentioned in long description)

    2011-08-26 - Tim Booth <tbooth@ceh.ac.uk> python-pynast (1.1-2ubuntu4) lucid; urgency=low * Fix Lintian warning on docs, clean up build file * Allow building with either python2 or python-central * Renamed main package to pynast

    2011-08-26 - Tim Booth <tbooth@ceh.ac.uk> python-pynast (1.1-2ubuntu3) lucid; urgency=low * Rebuild for Lucid, lowered dependencies

    2011-08-25 - Steffen Moeller <moeller@debian.org> python-pynast (1.1-2) unstable; urgency=low * Transition to dh7 and dh_python2 * Adjusted uploaders, first upload to unstable * Documentation built with sphinx * Added man page

    2010-07-25 - Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de> python-pynast (1.1-1) experimental; urgency=low * Initial release (Closes: #587189)

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