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* Clean up some thingsTobias Kortkamp2021-04-151-1/+0
| | | | | | | | | - Remove duplicate variables - Remove nop variables - Sort categories - Remove redundant option descriptions that match the default ones Reported by: portscan
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/phyml: fix build on recent currentTobias C. Berner2020-08-294-0/+74
| | | | | | | | | | mostly backport of: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a Obtained from: https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a Notes: svn path=/head/; revision=546884
* biology/phyml: update to 3.3.20200621Fernando Apesteguía2020-07-102-6/+5
| | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=541852
* - Swap back from net/openmpi3 to net/openmpiDanilo Egea Gondolfo2020-04-211-3/+3
| | | | Notes: svn path=/head/; revision=532429
* - Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.Danilo Egea Gondolfo2020-04-121-4/+4
| | | | Notes: svn path=/head/; revision=531485
* biology/phyml: disable -march=nativePiotr Kubaj2019-12-061-1/+2
| | | | | | | | | Ports shouldn't build for the host CPU, it also breaks compilation on non-x86. Approved by: mentors (implicit approval) Notes: svn path=/head/; revision=519139
* biology/phyml: update to 3.3.20190909Fernando Apesteguía2019-09-102-6/+6
| | | | | | | | | While here, add license. Reported by: portscout Notes: svn path=/head/; revision=511777
* - Update to 3.3.20190321Wen Heping2019-05-202-5/+4
| | | | Notes: svn path=/head/; revision=502098
* Change 4 ports from net/mpich2 to net/mpichYuri Victorovich2018-09-221-3/+5
| | | | | | | | | | mpich2 is the obsolete version 2.x, mpich is at the current version 3.x Ports: biology/phyml benchmarks/mdtest benchmarks/imb math/parmetis Notes: svn path=/head/; revision=480425
* biology/phyml: update to v3.3.20180621Fernando Apesteguía2018-06-232-5/+6
| | | | | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D15967 Notes: svn path=/head/; revision=473138
* - Update to 3.3.20180214Wen Heping2018-05-152-5/+6
| | | | Notes: svn path=/head/; revision=469992
* Remove now-useless, commented-out lines.Mark Linimon2018-03-101-4/+0
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=464132
* - Update to 3.3.20180129Wen Heping2018-02-012-5/+4
| | | | Notes: svn path=/head/; revision=460569
* Disable the extra flag "-march=native" on arm to fix builds.Mark Linimon2017-12-271-3/+6
| | | | | | | | Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com -exp run Notes: svn path=/head/; revision=457351
* These are also broken on aarch64 in the same way as armv6/7.Mark Linimon2017-12-091-0/+1
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455815
* Mark more ports broken that fail on both armv6 and armv7.Mark Linimon2017-12-091-0/+3
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455813
* Update to 3.3.20170530Sunpoet Po-Chuan Hsieh2017-09-042-3/+5
| | | | | | | Changes: https://github.com/stephaneguindon/phyml/releases Notes: svn path=/head/; revision=449234
* Update WWWSunpoet Po-Chuan Hsieh2017-05-301-1/+1
| | | | Notes: svn path=/head/; revision=442081
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-2/+2
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* - Update to 3.2.0Wen Heping2016-02-263-34/+62
| | | | | | | | | | - Update pkg-descr PR: 205890 Submitted by: tkato432@yahoo.com Notes: svn path=/head/; revision=409605
* Convert to USES=autoreconfBaptiste Daroussin2014-12-281-2/+2
| | | | Notes: svn path=/head/; revision=375747
* - Stage supportMartin Wilke2014-01-311-1/+0
| | | | Notes: svn path=/head/; revision=341987
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-0/+1
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - Remove MAKE_JOBS_SAFE variableAlex Kozlov2013-08-141-1/+0
| | | | | | | Approved by: portmgr (bdrewery) Notes: svn path=/head/; revision=324744
* - Update to 20121109.Marcelo Araujo2013-02-044-43/+25
| | | | | | | | PR: ports/175014 Submitted by: KATO Tsuguru <tkato432@yahoo.com> Notes: svn path=/head/; revision=311601
* - Reset MAINTAINER due to unrecoverable email bounceRyan Steinmetz2012-12-041-1/+1
| | | | | | | | Reported by: portscout Feature safe: yes Notes: svn path=/head/; revision=308268
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* Sync to new bsd.autotools.mkAde Lovett2010-12-041-1/+1
| | | | Notes: svn path=/head/; revision=265663
* Round one migration of ports from automake{19,110} to automake111Ade Lovett2010-10-051-1/+1
| | | | Notes: svn path=/head/; revision=262460
* PhyML is a software that estimates maximum likelihood phylogenies fromDmitry Marakasov2009-07-215-0/+74
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> Notes: svn path=/head/; revision=238140
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