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Port details
paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9i biology on this many watch lists=1 search for ports that depend on this port Find issues related to this port Report an issue related to this port 4.9iVersion of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2000-07-10 00:21:06
Last Update: 2019-02-26 15:12:43
SVN Revision: 493971
License: GPLv3
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (176 items)
  1. /usr/local/share/licenses/paml-4.9i/catalog.mk
  2. /usr/local/share/licenses/paml-4.9i/LICENSE
  3. /usr/local/share/licenses/paml-4.9i/GPLv3
  4. share/doc/paml/MCMCtree.Tutorials.pdf
  5. share/doc/paml/README.txt
  6. share/doc/paml/pamlDOC.pdf
  7. share/doc/paml/pamlFAQs.pdf
  8. share/doc/paml/pamlHistory.txt
  9. share/examples/paml/3s.trees
  10. share/examples/paml/4s.trees
  11. share/examples/paml/5s.trees
  12. share/examples/paml/6s.trees
  13. share/examples/paml/9s.trees
  14. share/examples/paml/CladeModelCD/ECP_EDN_15.nuc
  15. share/examples/paml/CladeModelCD/PAMLCladeModelCDnotes.pdf
  16. share/examples/paml/CladeModelCD/codeml.CladeC.ctl
  17. share/examples/paml/CladeModelCD/codeml.CladeD.ctl
  18. share/examples/paml/CladeModelCD/tree.txt
  19. share/examples/paml/DatingSoftBound/BF.Clock23.xlsx
  20. share/examples/paml/DatingSoftBound/BFdriverDOC.pdf
  21. share/examples/paml/DatingSoftBound/FixedDsClock23.txt
  22. share/examples/paml/DatingSoftBound/README.BayesFactor.txt
  23. share/examples/paml/DatingSoftBound/README.txt
  24. share/examples/paml/DatingSoftBound/bf1/mcmctree.ctl
  25. share/examples/paml/DatingSoftBound/bf2/mcmctree.ctl
  26. share/examples/paml/DatingSoftBound/mcmctree.Infinitesites.ctl
  27. share/examples/paml/DatingSoftBound/mcmctree.ctl
  28. share/examples/paml/DatingSoftBound/mtCDNApri.trees
  29. share/examples/paml/DatingSoftBound/mtCDNApri123.txt
  30. share/examples/paml/GeneticCode.txt
  31. share/examples/paml/HIVNSsites/HIVenvSweden.trees
  32. share/examples/paml/HIVNSsites/HIVenvSweden.txt
  33. share/examples/paml/HIVNSsites/HIVenvSweden4s.trees
  34. share/examples/paml/HIVNSsites/HIVenvSweden4s.txt
  35. share/examples/paml/HIVNSsites/README.txt
  36. share/examples/paml/HIVNSsites/codeml.ctl
  37. share/examples/paml/MCaa.dat
  38. share/examples/paml/MCbase.dat
  39. share/examples/paml/MCbaseRandomTree.dat
  40. share/examples/paml/MCcodon.dat
  41. share/examples/paml/MHC.Swanson2002MBE/README.txt
  42. share/examples/paml/MHC.Swanson2002MBE/bigmhc.phy
  43. share/examples/paml/MHC.Swanson2002MBE/bigmhc.trees
  44. share/examples/paml/MHC.Swanson2002MBE/codeml.ctl
  45. share/examples/paml/MouseLemurs/MouseLemurs.aa
  46. share/examples/paml/MouseLemurs/MouseLemurs.nuc
  47. share/examples/paml/MouseLemurs/MouseLemurs.trees
  48. share/examples/paml/MouseLemurs/MouseLemurs123.nuc
  49. share/examples/paml/MouseLemurs/README.txt
  50. share/examples/paml/MouseLemurs/README2.txt
  51. share/examples/paml/MouseLemurs/aaml.ctl
  52. share/examples/paml/MouseLemurs/aaml2.ctl
  53. share/examples/paml/MouseLemurs/baseml.ctl
  54. share/examples/paml/MouseLemurs/baseml2.ctl
  55. share/examples/paml/MouseLemurs/codeml.ctl
  56. share/examples/paml/MouseLemurs/codonml.ctl
  57. share/examples/paml/MouseLemurs/codonml2.ctl
  58. share/examples/paml/MouseLemurs/mtmam.dat
  59. share/examples/paml/README.txt
  60. share/examples/paml/Technical/Pt/eigenQREV.pdf
  61. share/examples/paml/Technical/Pt/testPMat.c
  62. share/examples/paml/Technical/Simulation/Codon/MCcodonNSbranches.dat
  63. share/examples/paml/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
  64. share/examples/paml/Technical/Simulation/Codon/MCcodonNSclade.dat
  65. share/examples/paml/Technical/Simulation/Codon/MCcodonNSsites.dat
  66. share/examples/paml/Technical/Simulation/Codon/PositiveSites.c
  67. share/examples/paml/Technical/Simulation/Codon/README.txt
  68. share/examples/paml/Technical/Simulation/Codon/codeml.ctl
  69. share/examples/paml/Technical/Simulation/multiruns.c
  70. share/examples/paml/Technical/Simulation/multiruns.txt
  71. share/examples/paml/TipDate.FluH1/H1.Beast.Nulldata.xml
  72. share/examples/paml/TipDate.FluH1/H1.Beast.xml
  73. share/examples/paml/TipDate.FluH1/H1.NodeNumbers.tre
  74. share/examples/paml/TipDate.FluH1/H1.nexus
  75. share/examples/paml/TipDate.FluH1/H1.tre
  76. share/examples/paml/TipDate.FluH1/H1.txt
  77. share/examples/paml/TipDate.FluH1/baseml.ctl
  78. share/examples/paml/TipDate.FluH1/commands.txt
  79. share/examples/paml/TipDate.FluH1/in.BV.HKYG5
  80. share/examples/paml/TipDate.FluH1/mcmctreeClock1.ctl
  81. share/examples/paml/TipDate.FluH1/mcmctreeClock2.ctl
  82. share/examples/paml/TipDate.FluH1/mcmctreeClock3.ctl
  83. share/examples/paml/TipDate.HIV2/FigTree.tre
  84. share/examples/paml/TipDate.HIV2/HIV2ge.tre
  85. share/examples/paml/TipDate.HIV2/HIV2ge.txt
  86. share/examples/paml/TipDate.HIV2/README.txt
  87. share/examples/paml/TipDate.HIV2/baseml.ctl
  88. share/examples/paml/TipDate.HIV2/in.BV.HKYG5
  89. share/examples/paml/TipDate.HIV2/mcmctree.ExactlnL.ctl
  90. share/examples/paml/TipDate.HIV2/mcmctree.ctl
  91. share/examples/paml/YN00abglobin.result
  92. share/examples/paml/aaml.ctl
  93. share/examples/paml/abglobin.aa
  94. share/examples/paml/abglobin.nuc
  95. share/examples/paml/abglobin.trees
  96. share/examples/paml/baseml.ctl
  97. share/examples/paml/brown.nuc
  98. share/examples/paml/brown.rooted.trees
  99. share/examples/paml/brown.trees
  100. share/examples/paml/codeml.ctl
  101. share/examples/paml/codonml.ctl
  102. share/examples/paml/dNdSGene1.nuc
  103. share/examples/paml/dat/MtZoa.dat
  104. share/examples/paml/dat/cpREV10.dat
  105. share/examples/paml/dat/cpREV64.dat
  106. share/examples/paml/dat/dayhoff-dcmut.dat
  107. share/examples/paml/dat/dayhoff.dat
  108. share/examples/paml/dat/g1974a.dat
  109. share/examples/paml/dat/g1974c.dat
  110. share/examples/paml/dat/g1974p.dat
  111. share/examples/paml/dat/g1974v.dat
  112. share/examples/paml/dat/grantham.dat
  113. share/examples/paml/dat/jones-dcmut.dat
  114. share/examples/paml/dat/jones.dat
  115. share/examples/paml/dat/lg.dat
  116. share/examples/paml/dat/miyata.dat
  117. share/examples/paml/dat/mtArt.dat
  118. share/examples/paml/dat/mtREV24.dat
  119. share/examples/paml/dat/mtmam.dat
  120. share/examples/paml/dat/wag.dat
  121. share/examples/paml/horai.nuc
  122. share/examples/paml/horai.trees
  123. share/examples/paml/lysin/README.txt
  124. share/examples/paml/lysin/RasMol.txt
  125. share/examples/paml/lysin/SiteNumbering.txt
  126. share/examples/paml/lysin/codeml.ctl
  127. share/examples/paml/lysin/codemlYangSwanson2002.ctl
  128. share/examples/paml/lysin/lysin.nuc
  129. share/examples/paml/lysin/lysin.trees
  130. share/examples/paml/lysin/lysinYangSwanson2002.nuc
  131. share/examples/paml/lysozyme/README.txt
  132. share/examples/paml/lysozyme/codeml.ctl
  133. share/examples/paml/lysozyme/lysozymeLarge.ctl
  134. share/examples/paml/lysozyme/lysozymeLarge.nuc
  135. share/examples/paml/lysozyme/lysozymeLarge.trees
  136. share/examples/paml/lysozyme/lysozymeSmall.ctl
  137. share/examples/paml/lysozyme/lysozymeSmall.nuc
  138. share/examples/paml/lysozyme/lysozymeSmall.trees
  139. share/examples/paml/lysozyme/lysozymeSmall.txt
  140. share/examples/paml/mcmctree.ctl
  141. share/examples/paml/mtCDNA/AAcodon.result.txt
  142. share/examples/paml/mtCDNA/README.txt
  143. share/examples/paml/mtCDNA/codeml.AAcodon.ctl
  144. share/examples/paml/mtCDNA/codeml.ctl
  145. share/examples/paml/mtCDNA/miyata.dat
  146. share/examples/paml/mtCDNA/mtCDNAmam.nuc
  147. share/examples/paml/mtCDNA/mtCDNAmam.trees
  148. share/examples/paml/mtCDNA/mtCDNApri.aa
  149. share/examples/paml/mtCDNA/mtCDNApri.nuc
  150. share/examples/paml/mtCDNA/mtCDNApri.trees
  151. share/examples/paml/mtCDNAape/2s.trees
  152. share/examples/paml/mtCDNAape/OmegaAA.dat
  153. share/examples/paml/mtCDNAape/README.txt
  154. share/examples/paml/mtCDNAape/codeml.HC.ctl
  155. share/examples/paml/mtCDNAape/codeml.ctl
  156. share/examples/paml/mtCDNAape/mtCDNA.HC.txt
  157. share/examples/paml/mtCDNAape/mtCDNAape.trees
  158. share/examples/paml/mtCDNAape/mtCDNAape.txt
  159. share/examples/paml/mtprim9.nuc
  160. share/examples/paml/pamp.ctl
  161. share/examples/paml/paupblock
  162. share/examples/paml/paupend
  163. share/examples/paml/paupstart
  164. share/examples/paml/stewart.aa
  165. share/examples/paml/stewart.trees
  166. share/examples/paml/yn00.ctl
  167. bin/baseml
  168. bin/basemlg
  169. bin/chi2
  170. bin/codeml
  171. bin/evolver
  172. bin/evolverNSbranches
  173. bin/evolverNSbranchsites
  174. bin/evolverNSsites
  175. bin/pamp
  176. bin/yn00
Collapse this list.
Dependency lines:
  • paml>0:biology/paml
To install the port: cd /usr/ports/biology/paml/ && make install clean
To add the package: pkg install paml
PKGNAME: paml
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. http://abacus.gene.ucl.ac.uk/software/

Number of commits found: 42

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Feb 2019 15:12:43
Original commit files touched by this commit  4.9i
Revision:493971
jrm search for other commits by this committer
biology/paml: Update to version 4.9i

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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
26 Apr 2018 15:36:31
Original commit files touched by this commit  4.9h
Revision:468355
jrm search for other commits by this committer
biology/paml: Set PORTVERSION directly

Setting DISTVERSION= 4.9h in the last commit caused PORTVERSION to be translated
to 4.9.h, which was not correct.

Pointy-hat: jrm
25 Apr 2018 20:36:39
Original commit files touched by this commit  4.9.h
Revision:468297
jrm search for other commits by this committer
biology/paml: Update to version 4.9h

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:
(Only the first 15 lines of the commit message are shown above View all of this commit message)
02 Nov 2016 22:45:14
Original commit files touched by this commit  4.9c_1
Revision:425174
mat search for other commits by this committer
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
29 Sep 2016 21:12:50
Original commit files touched by this commit  4.9c_1
Revision:422950
jrm search for other commits by this committer
Update PORTREVISION and dinstinfo due to upstream tarball change

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8083
28 Sep 2016 02:30:29
Original commit files touched by this commit  4.9c
Revision:422846
jrm search for other commits by this committer
biology/paml: update to version 4.9c and various improvements

- 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
23 Sep 2016 21:42:02
Original commit files touched by this commit  4.9a
Revision:422697
jrm search for other commits by this committer
Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995
19 May 2016 10:21:25
Original commit files touched by this commit  4.9a
Revision:415498
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
16 May 2016 16:10:36
Original commit files touched by this commit  4.9a
Revision:415338
amdmi3 search for other commits by this committer
- Update to 4.9a
- While here, simplify WRKSRC and use options helpers

PR:		209535
Submitted by:	jrm@ftfl.ca (maintainer)
10 Apr 2015 15:39:01
Original commit files touched by this commit  4.8a
Revision:383736
brd search for other commits by this committer
Update biology/paml to 4.8a and unbreak.

PR:		199264
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	bdrewery (mentor)
05 Apr 2015 17:55:36
Original commit files touched by this commit  4.8
Revision:383309
bapt search for other commits by this committer
Mark as broken unfetchable ports
19 Jan 2015 12:11:26
Original commit files touched by this commit  4.8
Revision:377397
wen search for other commits by this committer
- Pass maintainership to submitter

PR:		196859
Submitted by:	Joseph Mingrone<jrm@ftfl.ca>
20 Oct 2014 07:10:48
Original commit files touched by this commit  4.8
Revision:371237
bapt search for other commits by this committer
Cleanup plist
29 Jul 2014 19:11:53
Original commit files touched by this commit  4.8
Revision:363374
adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
05 Apr 2014 10:56:52
Original commit files touched by this commit  4.8
Revision:350214
wen search for other commits by this committer
- Update to 4.8
- Reset maintainer to ports@
14 Mar 2014 12:59:34
Original commit files touched by this commit  4.4c
Revision:348221
ehaupt search for other commits by this committer
Support staging
13 Mar 2014 07:41:34
Original commit files touched by this commit  4.4c
Revision:348042
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
21 Feb 2014 13:35:26
Original commit files touched by this commit  4.4c
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  4.4c
Revision:343634
ehaupt search for other commits by this committer
According to the Porter's Handbook (5.12.2.3.) default options must be added to
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)
21 Jan 2014 23:18:05
Original commit files touched by this commit  4.4c
Revision:340671
bapt search for other commits by this committer
Fix properties on pkg-plist
03 Jan 2014 15:46:52
Original commit files touched by this commit  4.4c
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  4.4c
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)
01 Jun 2013 14:22:36
Original commit files touched by this commit  4.4c
Revision:319570
wen search for other commits by this committer
- Trim Makefile headers
19 Mar 2011 12:38:54
Original commit files touched by this commit  4.4c

miwi search for other commits by this committer
- Get Rid MD5 support
08 Sep 2010 00:16:45
Original commit files touched by this commit  4.4c

wen search for other commits by this committer
- Update to 4.4c
20 Apr 2010 08:42:05
Original commit files touched by this commit  4.4a

wen search for other commits by this committer
- Update to 4.4a
- Update my mail address to FreeBSD
13 Aug 2009 17:00:04
Original commit files touched by this commit  4.3

miwi search for other commits by this committer
- Update to 4.3

PR:             137625
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
02 Mar 2009 19:02:49
Original commit files touched by this commit  4.2b

miwi search for other commits by this committer
- Update to 4.2b

PR:             132249
Submitted by:   Wen Heping <wenheping@gmail.com>
25 Dec 2008 19:56:07
Original commit files touched by this commit  4.2

miwi search for other commits by this committer
- Update to 4.2

PR:             129895
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
30 Sep 2008 08:54:55
Original commit files touched by this commit  4.1

miwi search for other commits by this committer
- Update to 4.1
- Pass maintainership to submitter

PR:             127683
Submitted by:   Wen heping <wenheping@gmail.com>
11 Mar 2007 03:21:18
Original commit files touched by this commit  3.15

linimon search for other commits by this committer
Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:            portmgr
20 May 2006 18:52:19
Original commit files touched by this commit  3.15

sem search for other commits by this committer
- Update to 3.15

PR:             ports/96941
Submitted by:   Paul Schmehl <pauls@utdallas.edu>
Approved by:    maintainer timeout
10 Nov 2005 01:21:42
Original commit files touched by this commit  3.14b

mnag search for other commits by this committer
Update to 3.14b
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
06 Nov 2004 03:55:37
Original commit files touched by this commit  3.14

kevlo search for other commits by this committer
Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>
31 Mar 2004 03:12:58
Original commit files touched by this commit  3.13

trevor search for other commits by this committer
SIZEify (maintainer timeout)
22 Oct 2003 09:29:55
Original commit files touched by this commit  3.13

osa search for other commits by this committer
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
14 Feb 2003 23:21:23
Original commit files touched by this commit  3.13

naddy search for other commits by this committer
* Update to 3.13.

PR:             48255
Submitted by:   David A. Bader <dbader@eece.unm.edu>

* Also honor CC/CFLAGS.
29 Aug 2001 13:00:08
Original commit files touched by this commit

wjv search for other commits by this committer
- Update to version 3.1    
03 Jul 2001 09:17:14
Original commit files touched by this commit

wjv search for other commits by this committer
Update to version 3.04    
02 Apr 2001 06:16:27
Original commit files touched by this commit

mharo search for other commits by this committer
update to 3.03    
08 Oct 2000 00:23:30
Original commit files touched by this commit

asami search for other commits by this committer
Convert category biology to new layout.  
10 Jul 2000 04:21:06
Original commit files touched by this commit

steve search for other commits by this committer
Add paml version 3.01.   A set of utilities for performing Phylogenetic Analysis
by Maximum   Likelihood (PAML).    

Number of commits found: 42

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