notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Ukraine
NOTE: the WWW: line in pkg-descr was relocated to a WWW= line in Makefile. Each port in FreshPorts has a homepage link. Look for it right after the Description: on each port's home page.

Do I know someone who can pick up a server from 7401 E. Ben White Blvd. Austin TX?

The emphasis is on know, or recommended by someone I know. This is the original FreshPorts server, way past useful: RAID, 8GB RAM, etc. The drives need to be wiped and everything recycled.
Port details
phyml Simple, fast, and accurate algorithm to estimate large phylogenies
3.3.20220408,1 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. pkg-fallout Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: GPLv3
Description:
HomepagecgitgithubgitlabSVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/phyml
  2. /usr/local/share/licenses/phyml-3.3.20220408,1/catalog.mk
  3. /usr/local/share/licenses/phyml-3.3.20220408,1/LICENSE
  4. /usr/local/share/licenses/phyml-3.3.20220408,1/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, 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:

Packages (timestamps in pop-ups are UTC):
phyml
ABIlatestquarterly
FreeBSD:11:aarch643.3.20180621_1,13.3.20190909_3,1
FreeBSD:11:amd643.3.20200621,13.3.20200621,1
FreeBSD:11:armv63.2.0,13.3.20190909_3,1
FreeBSD:11:i3863.3.20200621,13.3.20200621,1
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips643.2.0,13.3.20190909_3,1
FreeBSD:12:aarch643.3.20180621_1,1pkg-fallout
FreeBSD:12:amd643.3.20220408,13.3.20211231,1
FreeBSD:12:armv63.3.20180621_1,13.3.20200621,1
FreeBSD:12:armv73.3.20180621_1,13.3.20200621,1
FreeBSD:12:i3863.3.20220408,13.3.20211231,1
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips643.3.20180621_1,13.3.20190909_3,1
FreeBSD:12:powerpc64pkg-fallout3.3.20200621,1
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd643.3.20220408,13.3.20220408,1
FreeBSD:13:armv63.3.20200621,1pkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i3863.3.20220408,13.3.20220408,1
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips643.3.20200621,13.3.20200621,1
FreeBSD:13:powerpc643.3.20200621,13.3.20200621,1
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd643.3.20220408,1pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i3863.3.20220408,1pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc643.3.20200621,1pkg-fallout
FreeBSD:14:riscv643.3.20200621,1pkg-fallout
 

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>=2.71 : devel/autoconf
  3. automake>=1.16.5 : devel/automake
  4. libtoolize : devel/libtool
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/stephaneguindon/phyml/tar.gz/v3.3.20220408?dummy=/
Collapse this list.

Number of commits found: 37

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit 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)
3.3.20220408,1
07 Sep 2022 21:10:59
commit 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)
3.3.20220408,1
02 Sep 2022 07:57:11
commit hash:026150563ee449fc13d0363a5e25b14a888772e7commit hash:026150563ee449fc13d0363a5e25b14a888772e7commit hash:026150563ee449fc13d0363a5e25b14a888772e7 files touched by this commit
Wen Heping (wen) search for other commits by this committer
biology/phyml: Update to 3.3.20220408
3.3.20211231,1
20 Jul 2022 14:20:57
commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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 View all of this commit message)
3.3.20211231,1
02 Jan 2022 17:31:24
commit hash:59a8ef603d053f64e4067f3723feeeb60610bedbcommit hash:59a8ef603d053f64e4067f3723feeeb60610bedbcommit hash:59a8ef603d053f64e4067f3723feeeb60610bedb files touched by this commit
Fernando Apesteguía (fernape) search for other commits by this committer
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
commit hash:68b99b391349672d7f70e7ac89d430b8dbe32850commit hash:68b99b391349672d7f70e7ac89d430b8dbe32850commit hash:68b99b391349672d7f70e7ac89d430b8dbe32850 files touched by this commit
Tijl Coosemans (tijl) search for other commits by this committer
devel/automake: update to 1.16.5
3.3.20200621,1
15 Apr 2021 08:31:56
commit hash:ffbc3bd9376a3672e16eafddf55b233b8fed1674commit hash:ffbc3bd9376a3672e16eafddf55b233b8fed1674commit hash:ffbc3bd9376a3672e16eafddf55b233b8fed1674 files touched by this commit
Tobias Kortkamp (tobik) search for other commits by this committer
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
commit 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.
3.3.20200621,1
29 Aug 2020 08:34:28
Revision:546884Original commit files touched by this commit
tcberner search for other commits by this committer
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
Revision:541852Original commit files touched by this commit
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
3.3.20190909_3,1
21 Apr 2020 21:51:56
Revision:532429Original commit files touched by this commit
danilo search for other commits by this committer
- Swap back from net/openmpi3 to net/openmpi
3.3.20190909_2,1
12 Apr 2020 09:06:25
Revision:531485Original commit files touched by this commit
danilo search for other commits by this committer
- Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.
3.3.20190909_1,1
06 Dec 2019 13:04:41
Revision:519139Original commit files touched by this commit
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)
3.3.20190909,1
10 Sep 2019 21:04:16
Revision:511777Original commit files touched by this commit
fernape search for other commits by this committer
biology/phyml: update to 3.3.20190909

While here, add license.

Reported by:	portscout
3.3.20190321,1
20 May 2019 09:17:29
Revision:502098Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.3.20190321
3.3.20180621_1,1
22 Sep 2018 18:00:25
Revision:480425Original commit files touched by this commit
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
3.3.20180621,1
23 Jun 2018 15:53:55
Revision:473138Original commit files touched by this commit
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
3.3.20180214,1
15 May 2018 03:17:54
Revision:469992Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.3.20180214
3.3.20180129,1
10 Mar 2018 23:35:03
Revision:464132Original commit files touched by this commit
linimon search for other commits by this committer
Remove now-useless, commented-out lines.

Approved by:	portmgr (tier-2 blanket)
3.3.20180129,1
01 Feb 2018 07:26:57
Revision:460569Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.3.20180129
3.3.20170530,1
27 Dec 2017 07:36:05
Revision:457351Original commit files touched by this commit
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
3.3.20170530,1
09 Dec 2017 01:39:20
Revision:455815Original commit files touched by this commit
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)
3.3.20170530,1
09 Dec 2017 00:42:05
Revision:455813Original commit files touched by this commit
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)
3.3.20170530,1
04 Sep 2017 00:01:36
Revision:449234Original commit files touched by this commit
sunpoet search for other commits by this committer
Update to 3.3.20170530

Changes:	https://github.com/stephaneguindon/phyml/releases
3.2.0,1
30 May 2017 15:22:06
Revision:442081Original commit files touched by this commit
sunpoet search for other commits by this committer
Update WWW
3.2.0,1
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
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
3.2.0,1
26 Feb 2016 13:03:05
Revision:409605Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.2.0
- Update pkg-descr

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

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

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

Reported by:	portscout
Feature safe:	yes
20090706
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
20090706
04 Dec 2010 07:34:27
Original commit files touched by this commit
ade search for other commits by this committer
Sync to new bsd.autotools.mk
20090706
05 Oct 2010 19:57:56
Original commit files touched by this commit
ade search for other commits by this committer
Round one migration of ports from automake{19,110} to automake111
20090706
21 Jul 2009 01:10:13
Original commit files touched by this commit
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: 37