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Port details
iqtree Efficient phylogenomic software by maximum likelihood
1.6.5 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
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 21 Oct 2017 16:58:02
License: GPLv2
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.

WWW: http://www.iqtree.org/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (4 items)
  1. bin/iqtree
  2. /usr/local/share/licenses/iqtree-1.6.5/catalog.mk
  3. /usr/local/share/licenses/iqtree-1.6.5/LICENSE
  4. /usr/local/share/licenses/iqtree-1.6.5/GPLv2
  5. Collapse this list.

To install the port: cd /usr/ports/biology/iqtree/ && make install clean
To add the package: pkg install iqtree

PKGNAME: iqtree

distinfo:

TIMESTAMP = 1526045389
SHA256 (Cibiv-IQ-TREE-v1.6.5_GH0.tar.gz) = 1488cec17b2ce1e23dd4367c3a8d43c5d2ed3a965aba61d155034471fbd08154
SIZE (Cibiv-IQ-TREE-v1.6.5_GH0.tar.gz) = 4467567


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. cmake : devel/cmake
  2. ninja : devel/ninja
  3. eigen3.pc : math/eigen3
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for iqtree-1.6.5:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
cmake compiler:openmp eigen:3

Master Sites:
  1. https://codeload.github.com/Cibiv/IQ-TREE/tar.gz/v1.6.5?dummy=/

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
18 Jun 2018 01:48:46
Original commit files touched by this commit  1.6.5
Revision:472665
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)
11 May 2018 16:57:10
Original commit files touched by this commit  1.6.5
Revision:469673
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
30 Apr 2018 16:37:22
Original commit files touched by this commit  1.6.4
Revision:468714
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
23 Mar 2018 01:22:47
Original commit files touched by this commit  1.6.3
Revision:465330
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
10 Mar 2018 17:46:06
Original commit files touched by this commit  1.6.2_1
Revision:464084
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).
03 Mar 2018 03:15:24
Original commit files touched by this commit  1.6.2
Revision:463462
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
02 Jan 2018 16:49:24
Original commit files touched by this commit  1.6.1_2
Revision:457914
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
29 Dec 2017 17:14:07
Original commit files touched by this commit  1.6.1_1
Revision:457516
jrm search for other commits by this committer
biology/iqtree: Fix distinfo after upstream re-released v1.6.1
28 Dec 2017 18:37:06
Original commit files touched by this commit  1.6.1
Revision:457467
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
11 Dec 2017 07:18:48
Original commit files touched by this commit  1.6.b4_1
Revision:455927
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)
06 Nov 2017 14:24:39
Original commit files touched by this commit  1.6.b4_1
Revision:453620
mat search for other commits by this committer
Fix USE_GITHUB usage.

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

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

Number of commits found: 13

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