paml 4.4c biology =0

Phylogenetic Analysis by Maximum Likelihood (PAML)
Maintained by: wen@FreeBSD.org
Port Added: 10 Jul 2000 00:21:06
License: not specified in port

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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

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required To Build: devel/gmake
There are no ports dependent upon this port

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

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Configuration Options

     No options to configure

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Master Sites:

http://abacus.gene.ucl.ac.uk/software/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Get Rid MD5 support

- Update to 4.4c

- Update to 4.4a
- Update my mail address to FreeBSD

- Update to 4.3

PR:             137625
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)

- Update to 4.2b

PR:             132249
Submitted by:   Wen Heping <wenheping@gmail.com>

- Update to 4.2

PR:             129895
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)

- Update to 4.1
- Pass maintainership to submitter

PR:             127683
Submitted by:   Wen heping <wenheping@gmail.com>

Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:            portmgr

- Update to 3.15

PR:             ports/96941
Submitted by:   Paul Schmehl <pauls@utdallas.edu>
Approved by:    maintainer timeout

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

Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>

SIZEify (maintainer timeout)

Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992

* Update to 3.13.

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

* Also honor CC/CFLAGS.

- Update to version 3.1    

Update to version 3.04    

update to 3.03    

Convert category biology to new layout.  

Add paml version 3.01.   A set of utilities for performing Phylogenetic Analysis
by Maximum   Likelihood (PAML).    

12 vulnerabilities affecting 17 ports have been reported in the past 14 days

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