tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood

Property Value
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.


Package Version Architecture Repository
tree-puzzle_5.2-8build1_amd64.deb 5.2 amd64 Ubuntu Universe
tree-puzzle - - -


Name Value
libc6 >= 2.7
libsprng2 -


Type URL
Binary Package tree-puzzle_5.2-8build1_i386.deb
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




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

See Also

Package Description
tree_1.7.0-3_i386.deb displays an indented directory tree, in color
treeline_1.4.1-1.1_all.deb versatile tree-like structured custom data manager
treesheets_20150702~git1c77449b-1build1_i386.deb Data organizer that covers spreadsheets, mind mappers, and small databases
treetop_1.6.3-1_all.deb Ruby-based text parsing and interpretation (command-line utility)
treeviewx_0.5.1+20100823-3build1_i386.deb Displays and prints phylogenetic trees
treil_1.8-2.2build2_i386.deb tree structure into tiles
trend_1.3-1_i386.deb general-purpose, efficient trend graph
trickle_1.07-10ubuntu2_i386.deb user-space bandwidth shaper
trigger-rally-data_0.6.1-2_all.deb free 3D rally racing car game - data files
trigger-rally_0.6.2+dfsg-1_i386.deb free 3D rally racing car game
triggerhappy_0.3.4-2_i386.deb global hotkey daemon for Linux
trilinos-doc_12.4.2-2_all.deb object-oriented framework for large-scale problems - documentation
trimage_1.0.5-1.1_all.deb GUI and command-line interface to optimize image files
trimmomatic_0.35+dfsg-1_all.deb flexible read trimming tool for Illumina NGS data
trinity_1.6-2_i386.deb system call fuzz tester