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* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/paml: fix the build with LLVM 11Kyle Evans2020-08-201-0/+14
| | | | | | | | | | | | | | | | LLVM 11 switched from -fcommon to -fno-common by default. This revealed a slight misposition of names in paml.h, which caused one symbol per enum that's not used anywhere. The fix just moves the names back so that the enums are named that, rather than creating new unused symbols. Reviewed by: zeising Approved by: jrm (maintainer) MFH: 2020Q3 Notes: svn path=/head/; revision=545542
* biology/paml: Update to version 4.9jJoseph Mingrone2019-11-222-6/+4
| | | | | | | | | | | | | | | | | | | | | | | | | | | - Remove BROKEN=. Version 4.9i became unfetchable when the author pulled the tarball to prevent users from downloading a version with new, serious bugs. Upstream changes described by the author: - mcmctree: Initial values have ages that are too old, exceeding max bounds. In theory bounds in mcmctree are always soft so that the node ages will move to the area of posterior mode when burnin is long enough. In practice the poor starting values are problematic and requires long burn-in. I have rewritten the code for generating initial values to respect the min and max bounds specified in the fossil calibrations. - codeml: A bug introduced in 4.9i caused the clade labels ($) to be ignored. This affects the branch, branch-site and clade models. If your tree has branch labels (#) only and no clade models, everything will be fine. If you have used the clade label ($) in the tree with or without the branch label (#), either the program will abort or the results will be incorrect. The clade label ($) is supposed to label all branches in the clade as well as the branch itself, but all clade labels in the tree are ignored in 4.9i. Earlier versions are correct. Notes: svn path=/head/; revision=518150
* Mark a few ports BROKEN, unfetchableAntoine Brodin2019-11-061-0/+2
| | | | Notes: svn path=/head/; revision=516880
* biology/paml: Update to version 4.9iJoseph Mingrone2019-02-263-4/+6
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Upstream changes as described by the author: - mcmctree: I have added an option (duplication = 1) for dating a tree with both speciations and gene duplications, so that some nodes on the tree share divergence times. Nodes sharing ages are identified using labels in the tree file: #1, #2, .... I have yet to update the document about specification of the model. - mcmctree: The TipDate option was written for one locus or partition and never worked for more than two loci/partitions. I have edited the code so that it works for multiple partitions, some of which may be molecular and the others morphological. - codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7 (FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This option uses the observed codon or amino acid frequencies for the mutation-selection models of codon usage. Instead the program estimates the frequencies using maximum likeihood, which is what the option estFreq = 1 does. Look at the README file in the examples/mtCDNAape/ folder. - codeml clade model D: The bounds for the w (dN/dS) ratios in the first site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model D in 4.9b. The motivation for the bounds is that site class 0 represents strong purifying selection with a small w0, while site class 1 should include sites under weak purifying selection with a larger w1. However the bounds are arbitrary. In some datasets, the MLEs are found to be at the bounds, making the interpretation awkward. I have changed the bounds to the following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user should swap the estimates of w0 and w2 if w0 > w1. Notes: svn path=/head/; revision=493971
* biology/paml: Set PORTVERSION directlyJoseph Mingrone2018-04-261-1/+1
| | | | | | | | | | Setting DISTVERSION= 4.9h in the last commit caused PORTVERSION to be translated to 4.9.h, which was not correct. Pointy-hat: jrm Notes: svn path=/head/; revision=468355
* biology/paml: Update to version 4.9hJoseph Mingrone2018-04-253-27/+181
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Port Changes: - Add EXAMPLES option and install most files under EXAMPLESDIR - Add USES=dos2unix to fix DOS line endings Upstream Changes: Version 4.9h, March 2018 (*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for rates for loci. Since 4.9d, the program and the documentation are inconsistent about the two priors, and which value (0 or 1) means which prior. I have now checked the program and the documentation to make sure that they are consistent: prior = 0: gamma-Dirichlet (dos Reis 2014). This is the default. prior = 1: conditional i.i.d. prior (Zhu et al. 2015). I believe these two are similar especially if the number of loci (partitions) is large, but no serious comparisons between the two priors have been published. Thanks to Adnan Moussalli for pointing out the errors. (*) codeml. It was discovered that the mechanistic amino acid substitution model implemented in Yang et al. (1998; see table 3), specified by seqtype = 2 model = 6, has been broken for a long time, since version 3.0 (2000) at least. Version 2.0 (1999) seems to be correct. This means that the model become broken soon since it was published. I have now fixed this. This model of amino acid substitution starts from a Markov chain for codons and then aggregate the states and merge the synonymous codons into one state (the coded amino acid). This is an approximate formulation since the process after state aggregation is not Markovian anymore. I have now added another codon-based amino acid substitution model that treats amino acids as ambiguities codons. The model is specified by seqtype = 2 model = 5. This is an exact formulation. (*) codeml. The number of categories in the BEB calculation under M2 and M8 is unintentionally set to 4 rather than 10. I have changed this back to 10. The details of this calculation are in Yang et al. 2005 MBE. Version 4.9g, December 2017 (*) codeml. A bug caused the BEB calculation under the site model M8 (NSsites = 8) to be incorrect, with the program printing out warming messages like "strange: f[ 5] = -0.0587063 very small." This bug was introduced in version 4.9b and affects versions 4.9b-f. A different bug was introduced in version 4.9f that causes the log likelihood function under the site model M8 (NSsites = 8) to be calculated incorrectly. These are now fixed. Version 4.9f, October 2017 (*) baseml, nonhomogeneous models (nhomo & fix_kappa). Those models allow different branches on the tree to have different Q matrices. Roughly nhomo controls the base frequency parameters while gix_kappa controls kappa or the exchangeability parameters (a b c d e in GTR/REV, for example). I added the option (nhomo = 5, fix_kappa = 2), which lets the user to define branch types, so that branches of the same type have the same exchangeability parameters (a b c d e for GTR) and base composition parameters, while branches of different types have different parameters. Branch types are labeled (using # and $), 0, 1, 2, .... The labels should be consecutive positive integers. The old options nhomo = 3 or 4 work for some models like GTR, but not some other models which also have base composition parameters. In this update, I think those options should work with all those models. I have also edited the documentation (look for option variable nhomo for baseml). (*) baseml & codeml. i added an option fix_blength = 3 (proportional), which means that branch lengths will be proporational to those given in the tree file, and the proportionality factor is estimated by ML. (*) codeml. The program does not count the parameters correctly for model M0 when fix_kappa = 1. The bug was introduced in version 4.9c and affects versions 4.9c-e. This is now fixed. (*) codeml (seqtype = 2 model = 2). If you are analyzing multiple protein data sets (ndata > 1) under the empirical models such as wag, jtt, dayhoff. The results for the first data set are correct, but all later data sets are analyzed incorrectly under the corresponding +F models, that is, wag+F, jtt+F, dayhoff+F, etc. A bug in the program means that for the second and later data sets, the equilibrium amino acid frequencies are taken from the real data and not correctly set to those specified by the empirical models. I note that this bug was recorded in the update Version 3.14b, April 2005, but it was somehow not fixed, even in that version. This is now fixed. Thanks to Nick Goldman for reporting this again. (*) evolver (options 5, 6, 7 for simulating nucleotide, codon and amino acid alignments). If you choose the option of printing out the site pattern counts instead of the sequences (specified at the beginning of the control file such as MCbase.dat), and if you are simulating two or more alignments, the program crashes after finishing the first alignment. This is now fixed. (*) mcmctree. The program crashes if you have a mixture of morphological loci and molecular loci, if not all the morphological loci are before the molecular loci. I have now fixed this. I think this was never described anyway. Version 4.9e, March 2017 (*) Edited the readme files to change the license to GPL. (*) mcmctree. A bug was introduced in version 4.9b which causes the program to read the fossil calibration information in the tree file incorrectly, if joint (minimum and maximum) bounds are specified using the symbol '<' and '>'. If you use the notation "B()", "L()", and 'U()', the information is read correctly. This bug was introduced in version 4.9b and exists in 4.9c and 4.9d. Versions 4.9a and earlier were correct. Version 4.9d, February 2017 (*) mcmctree. Changed the default prior for rates for loci to gamma-Dirichlet (dos Reis 2014), and updated the documentation as well. It was set to the conditional i.i.d. prior (Zhu et al. 2015). (*) mcmctree. Added Bayes factor calculation. A program called BFdriver is included in the release, as well as a pdf document in the folder examples/DatingSoftBound/BFdriverDOC.pdf. We suggest that you use the exact likelihood calculation when you use this option, since the normal approximation is unreliable when the power posterior is close to the prior (when beta is small). Notes: svn path=/head/; revision=468297
* Cleanup no longer needed CHMOD usage after r424898.Mathieu Arnold2016-11-021-2/+1
| | | | | | | | | | PR: 213743 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight Notes: svn path=/head/; revision=425174
* Update PORTREVISION and dinstinfo due to upstream tarball changeJoseph Mingrone2016-09-292-3/+4
| | | | | | | | | Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8083 Notes: svn path=/head/; revision=422950
* biology/paml: update to version 4.9c and various improvementsJoseph Mingrone2016-09-284-33/+48
| | | | | | | | | | | | | | | | | | | | - Update to version 4.9c - Set LICENSE=GPLv3 - Use the variable PORTDOCS to automate the generation of the DOCS plist (as suggested by mat@). - Install dat/ examples/ and Technical/ directories as well as files in the root directory of the distribution tarball. - Fix broken permissions. - Delete Windows executables. - Build and install useful binaries not built by upstream's Makefile. - Update pkg-descr. Reviewed by: swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8040 Notes: svn path=/head/; revision=422846
* Update email address to jrm@FreeBSD.org for ports that I maintainJoseph Mingrone2016-09-231-1/+1
| | | | | | | | | Reviewed by: mat, swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D7995 Notes: svn path=/head/; revision=422697
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-191-4/+4
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415498
* - Update to 4.9aDmitry Marakasov2016-05-162-4/+7
| | | | | | | | | | - While here, simplify WRKSRC and use options helpers PR: 209535 Submitted by: jrm@ftfl.ca (maintainer) Notes: svn path=/head/; revision=415338
* Update biology/paml to 4.8a and unbreak.Brad Davis2015-04-102-7/+5
| | | | | | | | | PR: 199264 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: bdrewery (mentor) Notes: svn path=/head/; revision=383736
* Mark as broken unfetchable portsBaptiste Daroussin2015-04-051-0/+2
| | | | Notes: svn path=/head/; revision=383309
* - Pass maintainership to submitterWen Heping2015-01-191-1/+1
| | | | | | | | PR: 196859 Submitted by: Joseph Mingrone<jrm@ftfl.ca> Notes: svn path=/head/; revision=377397
* Cleanup plistBaptiste Daroussin2014-10-201-1/+0
| | | | Notes: svn path=/head/; revision=371237
* Convert a bunch of EXTRACT_SUFX=... into USES=tar:...Adam Weinberger2014-07-291-2/+1
| | | | | | | Approved by: portmgr (not really, but touches unstaged ports) Notes: svn path=/head/; revision=363374
* - Update to 4.8Wen Heping2014-04-053-8/+8
| | | | | | | - Reset maintainer to ports@ Notes: svn path=/head/; revision=350214
* Support stagingEmanuel Haupt2014-03-141-9/+3
| | | | Notes: svn path=/head/; revision=348221
* - Convert USE_GMAKE to USESMartin Wilke2014-03-131-1/+1
| | | | Notes: svn path=/head/; revision=348042
* Remove trailing whitespaces from category biologyEmanuel Haupt2014-02-211-1/+1
| | | | Notes: svn path=/head/; revision=345397
* According to the Porter's Handbook (5.12.2.3.) default options must be added toEmanuel Haupt2014-02-101-0/+2
| | | | | | | | | | | | | | OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt) Notes: svn path=/head/; revision=343634
* Fix properties on pkg-plistBaptiste Daroussin2014-01-211-1/+0
| | | | Notes: svn path=/head/; revision=340671
* Convert biology to MDOCS and MEXAMPLESAdam Weinberger2014-01-031-1/+4
| | | | Notes: svn path=/head/; revision=338550
* 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
* - Trim Makefile headersWen Heping2013-06-011-5/+1
| | | | Notes: svn path=/head/; revision=319570
* - Get Rid MD5 supportMartin Wilke2011-03-191-1/+0
| | | | Notes: svn path=/head/; revision=271305
* - Update to 4.4cWen Heping2010-09-082-4/+4
| | | | Notes: svn path=/head/; revision=260724
* - Update to 4.4aWen Heping2010-04-202-7/+7
| | | | | | | - Update my mail address to FreeBSD Notes: svn path=/head/; revision=252949
* - Update to 4.3Martin Wilke2009-08-132-6/+6
| | | | | | | | PR: 137625 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=239469
* - Update to 4.2bMartin Wilke2009-03-022-6/+6
| | | | | | | | PR: 132249 Submitted by: Wen Heping <wenheping@gmail.com> Notes: svn path=/head/; revision=229355
* - Update to 4.2Martin Wilke2008-12-252-4/+4
| | | | | | | | PR: 129895 Submitted by: Wen Heping <wenheping@gmail.com> (maintainer) Notes: svn path=/head/; revision=224766
* - Update to 4.1Martin Wilke2008-09-303-8/+13
| | | | | | | | | | - Pass maintainership to submitter PR: 127683 Submitted by: Wen heping <wenheping@gmail.com> Notes: svn path=/head/; revision=221025
* Reset dbader@eece.unm.edu due to maintainer-timeouts.Mark Linimon2007-03-111-1/+1
| | | | | | | Hat: portmgr Notes: svn path=/head/; revision=187091
* - Update to 3.15Sergey Matveychuk2006-05-202-4/+4
| | | | | | | | | PR: ports/96941 Submitted by: Paul Schmehl <pauls@utdallas.edu> Approved by: maintainer timeout Notes: svn path=/head/; revision=162900
* Update to 3.14bMarcus Alves Grando2005-11-102-9/+11
| | | | | | | | | | | | | Update MASTER_SITES Add SHA256 Remove extra TABS PR: 88007 Submitted by: Jean Milanez Melo <jmelo@freebsdbrasil.com.br> Approved by: maintainer timeout, 14 days Notes: svn path=/head/; revision=147771
* Update to 3.14Kevin Lo2004-11-063-5/+4
| | | | | | | | PR: ports/72422 Submitted by: Choe, Cheng-Dae <whitekid@gmail.com> Notes: svn path=/head/; revision=120935
* SIZEify (maintainer timeout)Trevor Johnson2004-03-311-0/+1
| | | | Notes: svn path=/head/; revision=105747
* Cosmetic fix: use %%DOCSDIR%% macro.Sergey A. Osokin2003-10-221-2/+2
| | | | | | | | | | No functionally changes. Submitted by: Oleg Karachevtsev <ok@etrust.ru> A part of PR: 57992 Notes: svn path=/head/; revision=91882
* * Update to 3.13.Christian Weisgerber2003-02-145-20/+7
| | | | | | | | | | PR: 48255 Submitted by: David A. Bader <dbader@eece.unm.edu> * Also honor CC/CFLAGS. Notes: svn path=/head/; revision=75540
* - Update to version 3.1Johann Visagie2001-08-294-6/+18
| | | | | | | | PR: 30176 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER) Notes: svn path=/head/; revision=47087
* Update to version 3.04Johann Visagie2001-07-033-5/+5
| | | | | | | | PR: 28614 Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER) Notes: svn path=/head/; revision=44678
* update to 3.03Michael Haro2001-04-024-27/+5
| | | | | | | | PR: 26094 Submitted by: maintainer Notes: svn path=/head/; revision=40710
* Add paml version 3.01.Steve Price2000-07-107-0/+89
A set of utilities for performing Phylogenetic Analysis by Maximum Likelihood (PAML). PR: 19753 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu> Notes: svn path=/head/; revision=30407
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