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Port details
phyml Simple, fast, and accurate algorithm to estimate large phylogenies
3.3.20200621,1 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. 3.3.20190909_3,1Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org
search for ports maintained by this maintainer
Port Added: 2009-07-21 01:10:33
Last Update: 2020-07-10 10:45:49
SVN Revision: 541852
License: GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
  1. bin/phyml
  2. /usr/local/share/licenses/phyml-3.3.20200621,1/catalog.mk
  3. /usr/local/share/licenses/phyml-3.3.20200621,1/LICENSE
  4. /usr/local/share/licenses/phyml-3.3.20200621,1/GPLv3
Collapse this list.
Dependency lines:
  • phyml>0:biology/phyml
To install the port: cd /usr/ports/biology/phyml/ && make install clean
To add the package: pkg install phyml
PKGNAME: phyml
Flavors: there is no flavor information for this port.
distinfo:
Packages: (move your mouse over the cells for more information)
phyml
ABIlatestquarterly
FreeBSD:11:aarch643.3.20180621_1,13.3.20190909_3,1
FreeBSD:11:amd643.3.20200621,13.3.20190909_3,1
FreeBSD:11:armv63.2.0,13.3.20190909_3,1
FreeBSD:11:i3863.3.20200621,13.3.20190909_3,1
FreeBSD:11:mips3.2.0,13.3.20190909_3,1
FreeBSD:11:mips643.2.0,13.3.20190909_3,1
FreeBSD:12:aarch643.3.20180621_1,13.3.20190909_3,1
FreeBSD:12:amd643.3.20200621,13.3.20190909_3,1
FreeBSD:12:armv63.3.20180621_1,13.3.20190909_3,1
FreeBSD:12:armv73.3.20180621_1,13.3.20190909_3,1
FreeBSD:12:i3863.3.20200621,13.3.20190909_3,1
FreeBSD:12:mips3.3.20180621_1,13.3.20190909_3,1
FreeBSD:12:mips643.3.20180621_1,13.3.20190909_3,1
FreeBSD:12:powerpc64-3.3.20190909_3,1
FreeBSD:13:aarch643.3.20190909_3,1-
FreeBSD:13:amd643.3.20200621,1-
FreeBSD:13:armv63.3.20190909_1,1-
FreeBSD:13:armv73.3.20190909_1,1-
FreeBSD:13:i3863.3.20200621,1-
FreeBSD:13:mips3.3.20190909_1,1-
FreeBSD:13:mips643.3.20200621,1-
FreeBSD:13:powerpc643.3.20200621,1-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. pkgconf>=1.3.0_1 : devel/pkgconf
  2. autoconf>=2.69 : devel/autoconf
  3. automake>=1.16.1 : devel/automake
  4. libtoolize : devel/libtool
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/stephaneguindon/phyml/tar.gz/v3.3.20200621?dummy=/

Number of commits found: 28

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Jul 2020 09:45:49
Original commit files touched by this commit  3.3.20200621,1
Revision:541852
fernape search for other commits by this committer
biology/phyml: update to 3.3.20200621

From ChangeLog:
https://github.com/stephaneguindon/phyml/releases/tag/v3.3.20200621

This release fixes a few minor bugs (see recent commits). The manual also gives
extra XML configuration information in order to apply fancy substitution models
(e.g., CAT-like) on single- or multiple-gene data sets

Reported by:	portscout
21 Apr 2020 21:51:56
Original commit files touched by this commit  3.3.20190909_3,1
Revision:532429
danilo search for other commits by this committer
- Swap back from net/openmpi3 to net/openmpi
12 Apr 2020 09:06:25
Original commit files touched by this commit  3.3.20190909_2,1
Revision:531485
danilo search for other commits by this committer
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.
06 Dec 2019 13:04:41
Original commit files touched by this commit  3.3.20190909_1,1
Revision:519139
pkubaj search for other commits by this committer
biology/phyml: disable -march=native

Ports shouldn't build for the host CPU, it also breaks compilation on non-x86.

Approved by:    mentors (implicit approval)
10 Sep 2019 21:04:16
Original commit files touched by this commit  3.3.20190909,1
Revision:511777
fernape search for other commits by this committer
biology/phyml: update to 3.3.20190909

While here, add license.

Reported by:	portscout
20 May 2019 09:17:29
Original commit files touched by this commit  3.3.20190321,1
Revision:502098
wen search for other commits by this committer
- Update to 3.3.20190321
22 Sep 2018 18:00:25
Original commit files touched by this commit  3.3.20180621_1,1
Revision:480425
yuri search for other commits by this committer
Change 4 ports from net/mpich2 to net/mpich

mpich2 is the obsolete version 2.x, mpich is at the current version 3.x

Ports:
biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis
23 Jun 2018 15:53:55
Original commit files touched by this commit  3.3.20180621,1
Revision:473138
fernape search for other commits by this committer
biology/phyml: update to v3.3.20180621

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D15967
15 May 2018 03:17:54
Original commit files touched by this commit  3.3.20180214,1
Revision:469992
wen search for other commits by this committer
- Update to 3.3.20180214
10 Mar 2018 23:35:03
Original commit files touched by this commit  3.3.20180129,1
Revision:464132
linimon search for other commits by this committer
Remove now-useless, commented-out lines.

Approved by:	portmgr (tier-2 blanket)
01 Feb 2018 07:26:57
Original commit files touched by this commit  3.3.20180129,1
Revision:460569
wen search for other commits by this committer
- Update to 3.3.20180129
27 Dec 2017 07:36:05
Original commit files touched by this commit  3.3.20170530,1
Revision:457351
linimon search for other commits by this committer
Disable the extra flag "-march=native" on arm to fix builds.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
09 Dec 2017 01:39:20
Original commit files touched by this commit  3.3.20170530,1
Revision:455815
linimon search for other commits by this committer
These are also broken on aarch64 in the same way as armv6/7.

Approved by:	portmgr (tier-2 blanket)
09 Dec 2017 00:42:05
Original commit files touched by this commit  3.3.20170530,1
Revision:455813
linimon search for other commits by this committer
Mark more ports broken that fail on both armv6 and armv7.

Approved by:	portmgr (tier-2 blanket)
04 Sep 2017 00:01:36
Original commit files touched by this commit  3.3.20170530,1
Revision:449234
sunpoet search for other commits by this committer
Update to 3.3.20170530

Changes:	https://github.com/stephaneguindon/phyml/releases
30 May 2017 15:22:06
Original commit files touched by this commit  3.2.0,1
Revision:442081
sunpoet search for other commits by this committer
Update WWW
01 Apr 2016 13:29:17
Original commit files touched by this commit  3.2.0,1
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
26 Feb 2016 13:03:05
Original commit files touched by this commit  3.2.0,1
Revision:409605
wen search for other commits by this committer
- Update to 3.2.0
- Update pkg-descr

PR:		205890
Submitted by:	tkato432@yahoo.com
28 Dec 2014 19:14:14
Original commit files touched by this commit  20121109
Revision:375747
bapt search for other commits by this committer
Convert to USES=autoreconf
31 Jan 2014 12:32:55
Original commit files touched by this commit  20121109
Revision:341987
miwi search for other commits by this committer
- Stage support
20 Sep 2013 15:55:44
Original commit files touched by this commit  20121109
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
14 Aug 2013 22:35:54
Original commit files touched by this commit  20121109
Revision:324744  Sanity Test Failure
ak search for other commits by this committer
- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)
04 Feb 2013 10:07:31
Original commit files touched by this commit  20121109
Revision:311601
araujo search for other commits by this committer
- Update to 20121109.

PR:		ports/175014
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
04 Dec 2012 20:28:16
Original commit files touched by this commit  20090706
Revision:308268
zi search for other commits by this committer
- Reset MAINTAINER due to unrecoverable email bounce

Reported by:	portscout
Feature safe:	yes
19 Mar 2011 12:38:54
Original commit files touched by this commit  20090706

miwi search for other commits by this committer
- Get Rid MD5 support
04 Dec 2010 07:34:27
Original commit files touched by this commit  20090706

ade search for other commits by this committer
Sync to new bsd.autotools.mk
05 Oct 2010 19:57:56
Original commit files touched by this commit  20090706

ade search for other commits by this committer
Round one migration of ports from automake{19,110} to automake111
21 Jul 2009 01:10:13
Original commit files touched by this commit  20090706

amdmi3 search for other commits by this committer
PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:             136877
Submitted by:   Ben Allen <ben@sysadminschronicles.com>

Number of commits found: 28

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