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.
===> The following configuration options are available for iqtree-3.1.4:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
biology/iqtree: Fix build with clang 21
Fix build by removing redundant instantiations of function templates in
terraphast/lib/clamped_uint.cpp.
Sponsored by: The FreeBSD Foundation
biology/iqtree: fix build on arm64
We call the platform "arm64", not "aarch64" (though it seems to be
inconsistent). Tested on powerpc64le, didn't build, as some
headers get confused by the whole "emulate SSE with Altivec" business.
Approved by: portmgr (build fix blanket)
MFH: 2026Q1
Sponsored by: Raptor Computing Systems, LLC
biology/iqtree: Update to 2.4.0
Refer to the release notes for information about a bug that may impact
past results.
PR: 284746
Release Notes: https://github.com/iqtree/iqtree2/releases/tag/v2.4.0
Sponsored by: The FreeBSD Foundation
Co-authored-by: Alven <alster@vinterdalen.se>
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)
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 )
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)
- 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
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
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
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
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
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
