progressivemauve_1.2.0+4713-2_amd64.deb


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Description

progressivemauve - multiple genome alignment algorithms

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe amd64
Package name: progressivemauve
Package version: 1.2.0+4713
Package release: 2
Package architecture: amd64
Package type: deb
Installed size: 5.09 KB
Download size: 829.50 KB
Official Mirror: archive.ubuntu.com
The mauveAligner and progressiveMauve alignment algorithms have been implemented as command-line programs included with the downloadable Mauve software. When run from the command-line, these programs provide options not yet available in the graphical interface. Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. Mauve computes and interactively visualizes genome sequence comparisons. Using FastA or GenBank sequence data, Mauve constructs multiple genome alignments that identify large-scale rearrangement, gene gain, gene loss, indels, and nucleotide substutition. Mauve is developed at the University of Wisconsin.

Alternatives

Replaces

  • mauvealigner <= 1.2.0+4713-1

    Download

    Source package: progressivemauve

    Install Howto

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

    Files

    • /usr/bin/addUnalignedIntervals
    • /usr/bin/alignmentProjector
    • /usr/bin/backbone_global_to_local
    • /usr/bin/bbAnalyze
    • /usr/bin/bbFilter
    • /usr/bin/coordinateTranslate
    • /usr/bin/createBackboneMFA
    • /usr/bin/extractBCITrees
    • /usr/bin/getAlignmentWindows
    • /usr/bin/getOrthologList
    • /usr/bin/makeBadgerMatrix
    • /usr/bin/mauveAligner
    • /usr/bin/mauveToXMFA
    • /usr/bin/mfa2xmfa
    • /usr/bin/progressiveMauve
    • /usr/bin/projectAndStrip
    • /usr/bin/randomGeneSample
    • /usr/bin/repeatoire
    • /usr/bin/scoreAlignment
    • /usr/bin/stripGapColumns
    • /usr/bin/stripSubsetLCBs
    • /usr/bin/toGrimmFormat
    • /usr/bin/toMultiFastA
    • /usr/bin/toRawSequence
    • /usr/bin/uniqueMerCount
    • /usr/bin/uniquifyTrees
    • /usr/bin/xmfa2maf
    • /usr/share/doc/progressivemauve/changelog.Debian.gz
    • /usr/share/doc/progressivemauve/copyright
    • /usr/share/man/man1/addUnalignedIntervals.1.gz
    • /usr/share/man/man1/alignmentProjector.1.gz
    • /usr/share/man/man1/backbone_global_to_local.1.gz
    • /usr/share/man/man1/bbAnalyze.1.gz
    • /usr/share/man/man1/bbFilter.1.gz
    • /usr/share/man/man1/coordinateTranslate.1.gz
    • /usr/share/man/man1/createBackboneMFA.1.gz
    • /usr/share/man/man1/extractBCITrees.1.gz
    • /usr/share/man/man1/getAlignmentWindows.1.gz
    • /usr/share/man/man1/getOrthologList.1.gz
    • /usr/share/man/man1/makeBadgerMatrix.1.gz
    • /usr/share/man/man1/mauveAligner.1.gz
    • /usr/share/man/man1/mauveToXMFA.1.gz
    • /usr/share/man/man1/mfa2xmfa.1.gz
    • /usr/share/man/man1/progressiveMauve.1.gz
    • /usr/share/man/man1/projectAndStrip.1.gz
    • /usr/share/man/man1/randomGeneSample.1.gz
    • /usr/share/man/man1/repeatoire.1.gz
    • /usr/share/man/man1/scoreAlignment.1.gz
    • /usr/share/man/man1/stripGapColumns.1.gz
    • /usr/share/man/man1/stripSubsetLCBs.1.gz
    • /usr/share/man/man1/toGrimmFormat.1.gz
    • /usr/share/man/man1/toMultiFastA.1.gz
    • /usr/share/man/man1/toRawSequence.1.gz
    • /usr/share/man/man1/uniqueMerCount.1.gz
    • /usr/share/man/man1/uniquifyTrees.1.gz
    • /usr/share/man/man1/xmfa2maf.1.gz

    Changelog

    2015-08-20 - Andreas Tille <tille@debian.org> progressivemauve (1.2.0+4713-2) unstable; urgency=medium * Rebuild against gcc-5 ported libmems Closes: #795239

    2015-05-20 - Andreas Tille <tille@debian.org> progressivemauve (1.2.0+4713-1) unstable; urgency=medium * Initial release to Debian (Closes: #783101)

    2015-04-19 - Andreas Tille <tille@debian.org> mauvealigner (1.2.0+4713-0ubuntu1) trusty; urgency=low * Initial upload to Debian Med PPA

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