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Port details
paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9h 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
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Jul 2000 00:21:06
License: GPLv3
Phylogenetic Analysis by Maximum Likelihood (PAML)

PAML is a package of programs for phylogenetic analyses of DNA or protein
sequences using maximum likelihood.  It is not good for tree making.  It may be
used to estimate parameters and test hypotheses for the study the evolutionary
process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY,
PhyML, or RaxML.

WWW: http://abacus.gene.ucl.ac.uk/software/paml.html
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (175 items)
  1. /usr/local/share/licenses/paml-4.9h/catalog.mk
  2. /usr/local/share/licenses/paml-4.9h/LICENSE
  3. /usr/local/share/licenses/paml-4.9h/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/HIV2ge.tre
  84. share/examples/paml/TipDate.HIV2/HIV2ge.txt
  85. share/examples/paml/TipDate.HIV2/README.txt
  86. share/examples/paml/TipDate.HIV2/baseml.ctl
  87. share/examples/paml/TipDate.HIV2/in.BV.HKYG5
  88. share/examples/paml/TipDate.HIV2/mcmctree.ExactlnL.ctl
  89. share/examples/paml/TipDate.HIV2/mcmctree.ctl
  90. share/examples/paml/YN00abglobin.result
  91. share/examples/paml/aaml.ctl
  92. share/examples/paml/abglobin.aa
  93. share/examples/paml/abglobin.nuc
  94. share/examples/paml/abglobin.trees
  95. share/examples/paml/baseml.ctl
  96. share/examples/paml/brown.nuc
  97. share/examples/paml/brown.rooted.trees
  98. share/examples/paml/brown.trees
  99. share/examples/paml/codeml.ctl
  100. share/examples/paml/codonml.ctl
  101. share/examples/paml/dNdSGene1.nuc
  102. share/examples/paml/dat/MtZoa.dat
  103. share/examples/paml/dat/cpREV10.dat
  104. share/examples/paml/dat/cpREV64.dat
  105. share/examples/paml/dat/dayhoff-dcmut.dat
  106. share/examples/paml/dat/dayhoff.dat
  107. share/examples/paml/dat/g1974a.dat
  108. share/examples/paml/dat/g1974c.dat
  109. share/examples/paml/dat/g1974p.dat
  110. share/examples/paml/dat/g1974v.dat
  111. share/examples/paml/dat/grantham.dat
  112. share/examples/paml/dat/jones-dcmut.dat
  113. share/examples/paml/dat/jones.dat
  114. share/examples/paml/dat/lg.dat
  115. share/examples/paml/dat/miyata.dat
  116. share/examples/paml/dat/mtArt.dat
  117. share/examples/paml/dat/mtREV24.dat
  118. share/examples/paml/dat/mtmam.dat
  119. share/examples/paml/dat/wag.dat
  120. share/examples/paml/horai.nuc
  121. share/examples/paml/horai.trees
  122. share/examples/paml/lysin/README.txt
  123. share/examples/paml/lysin/RasMol.txt
  124. share/examples/paml/lysin/SiteNumbering.txt
  125. share/examples/paml/lysin/codeml.ctl
  126. share/examples/paml/lysin/codemlYangSwanson2002.ctl
  127. share/examples/paml/lysin/lysin.nuc
  128. share/examples/paml/lysin/lysin.trees
  129. share/examples/paml/lysin/lysinYangSwanson2002.nuc
  130. share/examples/paml/lysozyme/README.txt
  131. share/examples/paml/lysozyme/codeml.ctl
  132. share/examples/paml/lysozyme/lysozymeLarge.ctl
  133. share/examples/paml/lysozyme/lysozymeLarge.nuc
  134. share/examples/paml/lysozyme/lysozymeLarge.trees
  135. share/examples/paml/lysozyme/lysozymeSmall.ctl
  136. share/examples/paml/lysozyme/lysozymeSmall.nuc
  137. share/examples/paml/lysozyme/lysozymeSmall.trees
  138. share/examples/paml/lysozyme/lysozymeSmall.txt
  139. share/examples/paml/mcmctree.ctl
  140. share/examples/paml/mtCDNA/AAcodon.result.txt
  141. share/examples/paml/mtCDNA/README.txt
  142. share/examples/paml/mtCDNA/codeml.AAcodon.ctl
  143. share/examples/paml/mtCDNA/codeml.ctl
  144. share/examples/paml/mtCDNA/miyata.dat
  145. share/examples/paml/mtCDNA/mtCDNAmam.nuc
  146. share/examples/paml/mtCDNA/mtCDNAmam.trees
  147. share/examples/paml/mtCDNA/mtCDNApri.aa
  148. share/examples/paml/mtCDNA/mtCDNApri.nuc
  149. share/examples/paml/mtCDNA/mtCDNApri.trees
  150. share/examples/paml/mtCDNAape/2s.trees
  151. share/examples/paml/mtCDNAape/OmegaAA.dat
  152. share/examples/paml/mtCDNAape/README.txt
  153. share/examples/paml/mtCDNAape/codeml.HC.ctl
  154. share/examples/paml/mtCDNAape/codeml.ctl
  155. share/examples/paml/mtCDNAape/mtCDNA.HC.txt
  156. share/examples/paml/mtCDNAape/mtCDNAape.trees
  157. share/examples/paml/mtCDNAape/mtCDNAape.txt
  158. share/examples/paml/mtprim9.nuc
  159. share/examples/paml/pamp.ctl
  160. share/examples/paml/paupblock
  161. share/examples/paml/paupend
  162. share/examples/paml/paupstart
  163. share/examples/paml/stewart.aa
  164. share/examples/paml/stewart.trees
  165. share/examples/paml/yn00.ctl
  166. bin/baseml
  167. bin/basemlg
  168. bin/chi2
  169. bin/codeml
  170. bin/evolver
  171. bin/evolverNSbranches
  172. bin/evolverNSbranchsites
  173. bin/evolverNSsites
  174. bin/pamp
  175. bin/yn00
  176. Collapse this list.

To install the port: cd /usr/ports/biology/paml/ && make install clean
To add the package: pkg install paml

PKGNAME: paml

distinfo:

TIMESTAMP = 1524675240
SHA256 (paml4.9h.tgz) = 623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3
SIZE (paml4.9h.tgz) = 6241149


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
===> The following configuration options are available for paml-4.9h:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
dos2unix gmake tar:tgz

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

Number of commits found: 41

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 41

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