Port details |
- phyml Simple, fast, and accurate algorithm to estimate large phylogenies
- 3.3.20220408_1,1 biology
=2 3.3.20220408_1,1Version 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
 - Port Added: 2009-07-21 01:10:33
- Last Update: 2024-06-16 15:25:18
- Commit Hash: 90c6e11
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/stephaneguindon/phyml
- Description:
- 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.
¦ ¦ ¦ ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/phyml/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/phyml
- pkg install phyml
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: phyml
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1662105216
SHA256 (stephaneguindon-phyml-v3.3.20220408_GH0.tar.gz) = 9cef375c0186e8a8d4db72ac02148707624c97174ffac244167a138ceb9f65bd
SIZE (stephaneguindon-phyml-v3.3.20220408_GH0.tar.gz) = 1803950
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- pkgconf>=1.3.0_1 : devel/pkgconf
- autoconf>=2.72 : devel/autoconf
- automake>=1.16.5 : devel/automake
- libtoolize : devel/libtool
- There are no ports dependent upon this port
Configuration Options:
- ===> The following configuration options are available for phyml-3.3.20220408_1,1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
====> MPI (Message Passing Interface) support: you can only select none or one of them
MPICH=off: Parallel processing support via MPICH 3
OPENMPI=off: Parallel processing support via Open MPI
===> Use 'make config' to modify these settings
- Options name:
- biology_phyml
- USES:
- autoreconf libtool pkgconfig
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
3.3.20220408_1,1 16 Jun 2024 15:25:18
    |
Piotr Kubaj (pkubaj)  |
biology/phyml: fix build on non-amd64
cc: error: unsupported option '-msse3' for target
'powerpc64-unknown-freebsd14.1' |
3.3.20220408_1,1 08 May 2023 08:25:50
    |
Robert Clausecker (fuz)  |
biology/phyml: fix build on non-x86
- only initialise x86-only fields on x86.
- make code compatible with platforms where char is unsigned
Obtained
from: https://github.com/stephaneguindon/phyml/commit/9c55b683c875fb9923e7cb2a1092596f72040882
MFH: 2023Q2 |
07 Sep 2022 21:58:51
    |
Stefan Eßer (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) |
3.3.20220408,1 07 Sep 2022 21:10:59
    |
Stefan Eßer (se)  |
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 ) |
3.3.20220408,1 02 Sep 2022 07:57:11
    |
Wen Heping (wen)  |
biology/phyml: Update to 3.3.20220408 |
3.3.20211231,1 20 Jul 2022 14:20:57
    |
Tobias C. Berner (tcberner)  |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
3.3.20211231,1 02 Jan 2022 17:31:24
    |
Fernando Apesteguía (fernape)  |
biology/phyml: update to 3.3.20211231
ChangeLog:
https://github.com/stephaneguindon/phyml/compare/v3.3.20211118...v3.3.20211231
Remove patches already merged into upstream.
Reported by: portscout |
3.3.20200621,1 12 Dec 2021 18:46:22
    |
Tijl Coosemans (tijl)  |
devel/automake: update to 1.16.5 |
3.3.20200621,1 15 Apr 2021 08:31:56
    |
Tobias Kortkamp (tobik)  |
Clean up some things
- Remove duplicate variables
- Remove nop variables
- Sort categories
- Remove redundant option descriptions that match the default ones
Reported by: portscan |
3.3.20200621,1 06 Apr 2021 14:31:07
    |
Mathieu Arnold (mat)  |
Remove # $FreeBSD$ from Makefiles. |
3.3.20200621,1 29 Aug 2020 08:34:28
  |
tcberner  |
biology/phyml: fix build on recent current
mostly backport of:
https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a
Obtained
from: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a |
3.3.20200621,1 10 Jul 2020 09:45:49
  |
fernape  |
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 |
3.3.20190909_3,1 21 Apr 2020 21:51:56
  |
danilo  |
- Swap back from net/openmpi3 to net/openmpi |
3.3.20190909_2,1 12 Apr 2020 09:06:25
  |
danilo  |
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated. |
3.3.20190909_1,1 06 Dec 2019 13:04:41
  |
pkubaj  |
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) |
3.3.20190909,1 10 Sep 2019 21:04:16
  |
fernape  |
biology/phyml: update to 3.3.20190909
While here, add license.
Reported by: portscout |
3.3.20190321,1 20 May 2019 09:17:29
  |
wen  |
- Update to 3.3.20190321 |
3.3.20180621_1,1 22 Sep 2018 18:00:25
  |
yuri  |
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 |
3.3.20180621,1 23 Jun 2018 15:53:55
  |
fernape  |
biology/phyml: update to v3.3.20180621
Approved by: tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D15967 |
3.3.20180214,1 15 May 2018 03:17:54
  |
wen  |
- Update to 3.3.20180214 |
3.3.20180129,1 10 Mar 2018 23:35:03
  |
linimon  |
Remove now-useless, commented-out lines.
Approved by: portmgr (tier-2 blanket) |
3.3.20180129,1 01 Feb 2018 07:26:57
  |
wen  |
- Update to 3.3.20180129 |
3.3.20170530,1 27 Dec 2017 07:36:05
  |
linimon  |
Disable the extra flag "-march=native" on arm to fix builds.
Approved by: portmgr (tier-2 blanket)
Obtained from: lonesome.com -exp run |
3.3.20170530,1 09 Dec 2017 01:39:20
  |
linimon  |
These are also broken on aarch64 in the same way as armv6/7.
Approved by: portmgr (tier-2 blanket) |
3.3.20170530,1 09 Dec 2017 00:42:05
  |
linimon  |
Mark more ports broken that fail on both armv6 and armv7.
Approved by: portmgr (tier-2 blanket) |
3.3.20170530,1 04 Sep 2017 00:01:36
  |
sunpoet  |
Update to 3.3.20170530
Changes: https://github.com/stephaneguindon/phyml/releases |
3.2.0,1 30 May 2017 15:22:06
  |
sunpoet  |
Update WWW |
3.2.0,1 01 Apr 2016 13:29:17
  |
mat  |
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight |
3.2.0,1 26 Feb 2016 13:03:05
  |
wen  |
- Update to 3.2.0
- Update pkg-descr
PR: 205890
Submitted by: tkato432@yahoo.com |
20121109 28 Dec 2014 19:14:14
  |
bapt  |
Convert to USES=autoreconf |
20121109 31 Jan 2014 12:32:55
  |
miwi  |
- Stage support |
20121109 20 Sep 2013 15:55:44
  |
bapt  |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
20121109 14 Aug 2013 22:35:54
  |
ak  |
- Remove MAKE_JOBS_SAFE variable
Approved by: portmgr (bdrewery) |
20121109 04 Feb 2013 10:07:31
  |
araujo  |
- Update to 20121109.
PR: ports/175014
Submitted by: KATO Tsuguru <tkato432@yahoo.com> |
20090706 04 Dec 2012 20:28:16
  |
zi  |
- Reset MAINTAINER due to unrecoverable email bounce
Reported by: portscout
Feature safe: yes |
20090706 19 Mar 2011 12:38:54
 |
miwi  |
- Get Rid MD5 support |
20090706 04 Dec 2010 07:34:27
 |
ade  |
Sync to new bsd.autotools.mk |
20090706 05 Oct 2010 19:57:56
 |
ade  |
Round one migration of ports from automake{19,110} to automake111 |
20090706 21 Jul 2009 01:10:13
 |
amdmi3  |
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> |