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Port details
paml Phylogenetic Analysis by Maximum Likelihood (PAML)
4.9a 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@ftfl.ca search for ports maintained by this maintainer
Port Added: 10 Jul 2000 00:21:06
License: not specified in port
Phylogenetic Analysis by Maximum Likelihood (PAML)

PAML is a program package for phylogenetic analyses of DNA or protein
sequences using maximum likelihood, and is maintained and distributed
by Ziheng Yang.

Possible uses of the programs are:
- Estimation of branch lengths in a phylogenetic tree and parameters
  in the evolutionary model such as the transition/transversion rate
  ratio, the shape parameter of the gamma distribution for variable
  evolutionary rates among sites, and rate parameters for different
  genes;
- Test of hypotheses concerning sequence evolution, such as rate
  constancy and independence among nucleotide or amino acid sites, rate
  constancy among lineages (the molecular clock), and homogeneity of
  evolutionary process in multiple genes;
- Calculation of substitution rates at sites;
- Reconstruction of ancestral nucleotide or amino acid sequences;
- Simulation of nucleotide, codon, and amino acid sequence data sets;
- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.

WWW: http://abacus.gene.ucl.ac.uk/software/paml.html
SVNWeb : Homepage : PortsMon

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

PKGNAME: paml


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-4.9a:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

USES:
gmake tar:tgz

Master Sites:
  1. http://abacus.gene.ucl.ac.uk/software/
  2. http://distcache.FreeBSD.org/ports-distfiles/

Number of commits found: 35

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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
files touched by this commit
wjv search for other commits by this committer
- Update to version 3.1    
03 Jul 2001 09:17:14
files touched by this commit
wjv search for other commits by this committer
Update to version 3.04    
02 Apr 2001 06:16:27
files touched by this commit
mharo search for other commits by this committer
update to 3.03    
08 Oct 2000 00:23:30
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
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: 35

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