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Port details
iqtree Efficient phylogenomic software by maximum likelihood
2.3.4 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.2.2.7Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-10-21 16:58:02
Last Update: 2024-05-16 16:08:07
Commit Hash: cbf6d59
License: GPLv2
WWW:
http://www.iqtree.org/
Description:
IQ-TREE is efficient and versatile phylogenomic software, created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). Development 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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/iqtree
  2. /usr/local/share/licenses/iqtree-2.3.4/catalog.mk
  3. /usr/local/share/licenses/iqtree-2.3.4/LICENSE
  4. /usr/local/share/licenses/iqtree-2.3.4/GPLv2
Collapse this list.
Dependency lines:
  • iqtree>0:biology/iqtree
To install the port:
cd /usr/ports/biology/iqtree/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/iqtree
  • pkg install iqtree
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: iqtree
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1715872647 SHA256 (iqtree-iqtree2-v.2.3.4_GH0.tar.gz) = 35bdac31c5795e5c72e532c2a311aa8266c9d40e7d668ee84c3b6e975af318da SIZE (iqtree-iqtree2-v.2.3.4_GH0.tar.gz) = 6568572

Expand this list (2 items)

Collapse this list.

SHA256 (tothuhien-lsd2-26ba127_GH0.tar.gz) = 63226da0e326d9fc47c54e8e380d48e51e923ccc25bd7f286d49b9f49028d1c4 SIZE (tothuhien-lsd2-26ba127_GH0.tar.gz) = 1079490

Collapse this list.


Packages (timestamps in pop-ups are UTC):
iqtree
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-2.3.4------
FreeBSD:13:quarterly-2.2.2.7------
FreeBSD:14:latest-2.3.4------
FreeBSD:14:quarterly-2.2.2.7------
FreeBSD:15:latest-2.3.4n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. ninja : devel/ninja
  3. eigen3.pc : math/eigen3
Library dependencies:
  1. libboost_filesystem.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options:
===> The following configuration options are available for iqtree-2.3.4: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings
Options name:
biology_iqtree
USES:
cmake eigen:3
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/iqtree/iqtree2/tar.gz/v.2.3.4?dummy=/
Collapse this list.

Number of commits found: 42

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.3.4
16 May 2024 16:08:07
commit hash: cbf6d5924f630508d156bf651a13caf54c78273dcommit hash: cbf6d5924f630508d156bf651a13caf54c78273dcommit hash: cbf6d5924f630508d156bf651a13caf54c78273dcommit hash: cbf6d5924f630508d156bf651a13caf54c78273d files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/iqtree: Update to 2.3.4

Release notes:	https://github.com/iqtree/iqtree2/releases/tag/v.2.3.4
Sponsored by:	The FreeBSD Foundation
2.3.2
14 Apr 2024 19:38:43
commit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985dcommit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985dcommit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985dcommit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985d files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/iqtree: Update to 2.3.2

Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.3.2
                https://github.com/iqtree/iqtree2/releases/tag/v2.3.1
Sponsored by:	The FreeBSD Foundation
2.2.2.7
05 Sep 2023 02:45:37
commit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aedcommit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aedcommit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aedcommit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aed files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
biology/iqtree: Update to 2.2.2.7

Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.2.2.7
Sponsored by:	The FreeBSD Foundation
2.0.6_5
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.0.6_4
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0.6_4
12 Aug 2022 14:46:53
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
2.0.6_3
22 May 2022 20:17:16
commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
2.0.6_2
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.0.6_2
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.0.6_2
12 Jan 2021 18:12:13
Revision:561368Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build

- USES=compiler:openmp still forces building with GCC.  This is no longer
  necessary on tier 1 platforms, which have openmp in base.

- Mark broken on i386, because base clang doesn't have 64 bit atomic
  functions for i386 (see bug 230888).

PR:		247753, 252379
Submitted by:	cmt (based on)
2.0.6_1
12 Dec 2020 17:04:37
Revision:557839Original commit files touched by this commit
thierry search for other commits by this committer
- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run
2.0.6
30 May 2020 18:43:26
Revision:537101Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 2.0.6

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6
2.0.5
28 May 2020 00:27:14
Revision:536729Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 2.0.5

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.5

While here, incorporate portfmt suggestions.
2.0.4
02 May 2020 20:32:34
Revision:533706Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 2.0.4
1.6.12
27 Aug 2019 01:19:11
Revision:509979Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.12

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12
1.6.11_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
1.6.11
24 Jun 2019 21:47:35
Revision:505061Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.11

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.11
1.6.10
21 Feb 2019 14:33:43
Revision:493504Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.10

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10
1.6.9_1
27 Dec 2018 18:34:44
Revision:488558Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: switch to outsource cmake build
1.6.9_1
26 Dec 2018 09:06:35
Revision:488363Original commit files touched by this commit
tcberner search for other commits by this committer
Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7
1.6.9
25 Dec 2018 20:25:40
Revision:488341Original commit files touched by this commit
tcberner search for other commits by this committer
Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine
1.6.9
23 Dec 2018 13:21:12
Revision:488217Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.9

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
1.6.8_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
1.6.8
28 Oct 2018 22:00:18
Revision:483358Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.8

Upstream release notes:
https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
1.6.7.1
16 Oct 2018 13:49:54
Revision:482228Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.7.1

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
1.6.7
27 Aug 2018 01:20:29
Revision:478170Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.7

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7
1.6.6_1
29 Jul 2018 22:18:46
Revision:475857Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
1.6.6
08 Jul 2018 21:15:47
Revision:474201Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.6

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6
1.6.5
18 Jun 2018 01:48:46
Revision:472665Original commit files touched by this commit
linimon search for other commits by this committer
Mark ports broken on powerpc64, categories a-c.

While here, pet portlint and do some other cleanup.

Approved by:	portmgr (tier-2 blanket)
1.6.5
11 May 2018 16:57:10
Revision:469673Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.5

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5
1.6.4
30 Apr 2018 16:37:22
Revision:468714Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.4

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4
1.6.3
23 Mar 2018 01:22:47
Revision:465330Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.3

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3
1.6.2_1
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
1.6.2
03 Mar 2018 03:15:24
Revision:463462Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.2

Upstream changes: http://www.iqtree.org/release/v1.6.2
1.6.1_2
02 Jan 2018 16:49:24
Revision:457914Original commit files touched by this commit
tcberner search for other commits by this committer
New USES=eigen

  Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it
to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702
1.6.1_1
29 Dec 2017 17:14:07
Revision:457516Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Fix distinfo after upstream re-released v1.6.1
1.6.1
28 Dec 2017 18:37:06
Revision:457467Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.1

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
1.6.b4_1
11 Dec 2017 07:18:48
Revision:455927Original commit files touched by this commit
linimon search for other commits by this committer
Mark several ports newly broken on arm.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
1.6.b4_1
06 Nov 2017 14:24:39
Revision:453620Original commit files touched by this commit
mat search for other commits by this committer
Fix USE_GITHUB usage.

Sponsored by:	Absolight
1.6.b4_1
21 Oct 2017 17:40:19
Revision:452596Original commit files touched by this commit
jrm search for other commits by this committer
biology/iqtree: Add EXAMPLES option and fix mess with installation of
example files in first commit
1.6.b4
21 Oct 2017 16:57:53
Revision:452595Original commit files touched by this commit
jrm search for other commits by this committer
New port, biology/iqtree: Efficient phylogenomic software

WWW: http://www.iqtree.org/

Number of commits found: 42