tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: tree-puzzle
Package version: 5.2
Package release: 8build1
Package architecture: i386
Package type: deb
Installed size: 296 B
Download size: 112.28 KB
Official Mirror:
TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.



    Source package: tree-puzzle

    Install Howto

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


    • /usr/bin/tree-puzzle
    • /usr/share/doc/tree-puzzle/AUTHORS
    • /usr/share/doc/tree-puzzle/README
    • /usr/share/doc/tree-puzzle/README.Debian
    • /usr/share/doc/tree-puzzle/changelog.Debian.gz
    • /usr/share/doc/tree-puzzle/copyright
    • /usr/share/man/man1/tree-puzzle.1.gz
    • /usr/share/menu/tree-puzzle
    • /usr/share/pixmaps/tree-puzzle.xpm


    2016-02-07 - Matthias Klose <> tree-puzzle (5.2-8build1) xenial; urgency=medium * No-change rebuild for openmpi transition.

    2015-11-25 - Andreas Tille <> tree-puzzle (5.2-8) unstable; urgency=low * debian/upstream: Add publications * cme fix dpkg-control * debhelper 9 * fix clean target when running test suite * Use dh_autoreconf to update for new architectures Closes: #765262 * Try hard to run the test suite * DEP5 copyright * Enable separate arch independet builds Closes: #806119

    2011-12-06 - Andreas Tille <> tree-puzzle (5.2-7) unstable; urgency=low * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields - Do not Build-Depend cdbs, quilt any more * Debhelper 8 (control + compat) * debian/source/format: 3.0 (quilt) * debian/rules: short dh * removed debian/README.source which becomes superfluous by using source format 3.0 (quilt) * debian/*.docs: Leave AUTHOR+README in the binary packages * Use Debian menu instead of desktop files to not confuse Gnome users Closes: #640003

    2009-11-10 - Andreas Tille <> tree-puzzle (5.2-6) unstable; urgency=low * Try to build against libopenmpi-dev instead of lam4-dev * Standards-Version: 3.8.3 (added debian/README.source) * Debhelper 7 * debian/rules: remove some outdated comments

    2009-03-31 - Andreas Tille <> tree-puzzle (5.2-5) unstable; urgency=low * Standards-Version: 3.8.1 (no changes needed) * Build against Debian's libsprng2-dev instead of a private copy of an outdated sprng Closes: #489678 * Build-Depends quilt instead of patchutils * No versioned Build-Depends of debhelper * tree-ppuzzle: Depends: lam-runtime

    2008-07-07 - Charles Plessy <> tree-puzzle (5.2-4) unstable; urgency=low * Changed the doc-base section according to the new policy. * debian/control: - Added myself to the `Uploaders' field. - Using debhelper 5. - Removed version inforation when the condition is satisfied even in oldsable (Sarge). - Checked conformance with Policy 3.8.0 (no changes needed). * debian/rules: include /usr/share/cdbs/1/class/ * debian/patches removed as their function is provided by CDBS.

    2008-03-02 - Andreas Tille <> tree-puzzle (5.2-3) unstable; urgency=low * Group maintenance according to Debian-Med group policy * Do not auto generate debian/control * Standards-Version: 3.7.3 (no changes needed) * Removed XB-Tag which is not used * Moved Homepage tag from description to control tags * Removed [Biology] from short description * Moved tree-puzzle-doc to section doc * Added watch file * debian/copyright: added Copyright statement

    2006-09-10 - Andreas Tille <> tree-puzzle (5.2-2) unstable; urgency=low * Standards-Version: 3.7.2 (no changes necessary) * Switched to cdbs * Desktop file * DebTags * Build-Depends: lam4-dev to enable building parallelized version * Split into two binary packages (normal and parallelized) version and extra documentation package. * Removed {Provides,Replaces,Conflicts}: puzzle because there is no such package in the thre previous releases an it causes trouble if both versions should be installed

    2004-07-15 - Andreas Tille <> tree-puzzle (5.2-1) unstable; urgency=low * New upstream version

    2004-07-14 - Andreas Tille <> tree-puzzle (5.1-1) unstable; urgency=low * New upstream version * Standards: 3.6.1 * Enhanced use of debhelper scripts