iqtree3 3.1.4+dfsg-1
Package Information
| Description | efficient phylogenetic software by maximum likelihood; v3 The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis. As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL. Key features of IQ-TREE - Efficient search algorithm: Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (Nguyen et al., 2015). - Ultrafast bootstrap: An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values (Minh et al., 2013). - Accurate model selection: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder (Kalyaanamoorthy et al., 2017). - Alignment simulation: A flexible simulator (AliSim) which allows to simulate sequence alignments under more realistic models than Seq-Gen and INDELible (Ly-Trong et al., 2023). - Phylogenetic testing: Several fast branch tests like SH-aLRT and aBayes test (Anisimova et al., 2011) and tree topology tests like the approximately unbiased (AU) test (Shimodaira, 2002). The strength of IQ-TREE is the availability of a wide variety of phylogenetic models: - Common models: All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites and ascertainment bias correction for e.g. SNP data. - Partition models: Allowing individual models for different genomic loci (e.g. genes or codon positions), mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths between partitions. - Mixture Models: fully customizable mixture models and empirical protein mixture models and. - Polymorphism-aware models (PoMo) http://www.iqtree.org/doc/Polymorphism-Aware-Models |
|---|---|
| Maintainer | Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> |
| Changed By | Andreas Tille <tille@debian.org> |
| Sponsor | tille@debian.org |
| Distribution | unstable |
| Architecture | amd64 arm64 |
| VCS | git: https://salsa.debian.org/med-team/iqtree3.git (browse) |
| Popcon Installs | 1 |
| Binary NEW | Yes (binary-only upload) |
| Tracker | https://tracker.debian.org/pkg/iqtree3 |
| Uploaded | 4 hours ago |
New Package Report
.changes
| Distribution | unstable |
|---|---|
| Date | Sun, 20 Sep 2026 20:00:22 +0200 |
| Source | iqtree3 |
| Version | 3.1.4+dfsg-1 |
| Changed-By | Andreas Tille |
| Architecture | source amd64 |
Changelog
iqtree3 (3.1.4+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Simplify watch file
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* New Build-Depends: libcmaple-dev, liblsd2-dev
* Deactivate help2man created manpages
* Build shared libiqtree.so.<SOVERSION> library and provide
new binary packages libiqtree3 and libiqtree-dev so that
python-cogent/piqtree can link against IQ-TREE
* Make build reproducible by deriving the embedded build date from
SOURCE_DATE_EPOCH instead of the __DATE__ macro
* Make build reproducible by disabling -march=native in the
terraphast sub-library, which otherwise makes the binaries depend
on the CPU of the build machine
* Remove binaries for several architectures in test_scripts/iqtree2.dsc
| Section | science |
|---|---|
| Priority | optional |
| Component | main |
| Package-List | iqtree3 deb science optional arch=amd64,arm64 libiqtree-dev deb libdevel optional arch=amd64,arm64 libiqtree3 deb libs optional arch=amd64,arm64 |
debian/copyright
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: IQ-TREE
Upstream-Contact: Lam Tung Nguyen <tung.nguyen@univie.ac.at>,
Bui Quang Minh <minh.bui@univie.ac.at>
Source: https://github.com/iqtree/iqtree3
Files-Excluded: lib*/*
zlib-*
doc/*
yaml-cpp/*
nn_models/*
*/.*
test_scripts/iqtree2
Files: *
Copyright: 2013-2018 Lam Tung Nguyen <tung.nguyen@univie.ac.at>
Heiko A. Schmidt <heiko.schmidt@mfpl.ac.at>
Arndt von Haeseler <arndt.von.haeseler@mfpl.ac.at>
Bui Quang Minh <minh.bui@mfpl.ac.at>
2006,2008 Steffen Klaere
2020 James Barbetti <james_barbettii@yahoo.com>
2018 Lukasz Reszczynski <lukasz.reszczynski@univie.ac.at>
License: GPL-2+
Files: utils/gzstream.*
Copyright: 2001 Deepak Bandyopadhyay, Lutz Kettner
License: LGPL-2.1+
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
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On Debian systems you can find the full text of the GNU Lesser General
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Files: lbfgsb/*
Copyright: 2014 Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230
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License version 3 as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.html), except
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The following additional terms apply under clause 7 of that license:
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OR IMPOSES OBLIGATIONS OR LIABILITY ON CSIRO THAT CANNOT BE EXCLUDED, RESTRICTED OR MODIFIED TO THE FULL EXTENT
SET OUT IN THE EXPRESS TERMS OF THIS CLAUSE ABOVE "CONSUMER GUARANTEES". TO THE EXTENT THAT SUCH CONSUMER
GUARANTEES CONTINUE TO APPLY, THEN TO THE FULL EXTENT PERMITTED BY THE APPLICABLE LEGISLATION, THE LIABILITY
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The following third party components are distributed with the Software. You agree to comply with the license
terms for these components as part of accessing the Software. Other third party software may also be identified
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R : A Computer Language for Statistical Data Analysis version 3.0.1 (http://cran.r-project.org/src/base/R-3/R-3.0.1.tar.gz)
Copyright (C) 2000-2004 The R Core Team
This software is licensed under GNU GPL
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JACOBI_EIGENVALUE.C (http://people.sc.fsu.edu/~jburkardt/c_src/jacobi_eigenvalue/jacobi_eigenvalue.c)
Copyright (C) 2003-2013 John Burkardt
This software is licensed under GNU LGPL (http://www.gnu.org/licenses/lgpl.html)
Files: ncl/*
Copyright: 1999-2003 Paul O. Lewis
License: GPL-2+
Files: pll/*
Copyright: 2013 Tomas Flouri and Alexandros Stamatakis
License: GPL-3+
Files: sprng/*
Copyright: 2000 Mascagni, Michael and Srinivasan, Ashok
License: NCSA
Disclaimer: NCSA expressly disclaims any and all warranties, expressed
or implied, concerning the enclosed software. The intent in sharing
this software is to promote the productive interchange of ideas
throughout the research community. All software is furnished on an
"as is" basis. No further updates to this software should be
expected. Although this may occur, no commitment exists. The authors
certainly invite your comments as well as the reporting of any bugs.
NCSA cannot commit that any or all bugs will be fixed.
Comment: The license statement was obtained from the libsprng2 package
of Debian. The code here is an incompatible copy of this library.
Upstream is informed and will enable using the Debian packaged version
in the next release of iqtree.
Files: vectorclass/*
Copyright: 2012-2014 Agner Fog
License: GPL-3+
Files: whtest/*
Copyright: 2009 Gunter Weiss, BUI Quang Minh, Arndt von Haeseler
License: GPL-2+
Files: terraphast/catch/catch.hpp
Copyright: Copyright (c) 2012 Two Blue Cubes Ltd.
License: Boost-1.0
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by
this license (the "Software") to use, reproduce, display, distribute,
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Software, and to permit third-parties to whom the Software is furnished to
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The copyright notices in the Software and this entire statement, including
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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Files: debian/*
Copyright: 2015-2018 Andreas Tille <tille@debian.org>
License: GPL-2+
Files: debian/Documents_source/*.tex
Copyright: 2013-2015 Lam Tung Nguyen <tung.nguyen@univie.ac.at>
Heiko A. Schmidt <heiko.schmidt@mfpl.ac.at>
Arndt von Haeseler <arndt.von.haeseler@mfpl.ac.at>
Bui Quang Minh <minh.bui@mfpl.ac.at>
License: GPL-2+
License: GPL-2+
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
On Debian systems you can find the full text of the GNU General Public
License version 2 or later at `/usr/share/common-licenses/GPL-2`.
License: GPL-3+
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option)
any later version.
.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
.
On Debian systems you can find the full text of the GNU General Public
License version 3 or later at `/usr/share/common-licenses/GPL-3`.