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FreeBSD biology : paml

Phylogenetic Analysis by Maximum Likelihood (PAML)

 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.  

paml history

v. 1.9
date: 2007/03/11 03:21:17;  author: linimon;  state: Exp;  lines: +1 -1
Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:		portmgr

v. 1.8
date: 2006/05/20 18:52:19;  author: sem;  state: Exp;  lines: +1 -1
- Update to 3.15

PR:		ports/96941
Submitted by:	Paul Schmehl 
Approved by:	maintainer timeout

v. 1.7
date: 2005/11/10 01:21:42;  author: mnag;  state: Exp;  lines: +8 -7
Update to 3.14b
Update MASTER_SITES
Add SHA256
Remove extra TABS

PR:		88007
Submitted by:	Jean Milanez Melo 
Approved by:	maintainer timeout, 14 days

v. 1.6
date: 2004/11/06 03:55:37;  author: kevlo;  state: Exp;  lines: +2 -2
Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae 

v. 1.5
date: 2003/02/14 23:21:23;  author: naddy;  state: Exp;  lines: +6 -6
* Update to 3.13.

PR:		48255
Submitted by:	David A. Bader 

* Also honor CC/CFLAGS.

v. 1.4
date: 2001/08/29 12:00:07;  author: wjv;  state: Exp;  lines: +5 -5
- Update to version 3.1

PR:		30176
Submitted by:	David A. Bader  (MAINTAINER)

v. 1.3
date: 2001/07/03 08:17:14;  author: wjv;  state: Exp;  lines: +3 -3
Update to version 3.04

PR:		28614
Submitted by:	David A. Bader  (MAINTAINER)

v. 1.2
date: 2001/04/02 05:16:26;  author: mharo;  state: Exp;  lines: +5 -5
update to 3.03

PR:		26094
Submitted by:	    maintainer

v. 1.1
date: 2000/07/10 03:21:00;  author: steve;  state: Exp;
Add paml version 3.01.
A set of utilities for performing Phylogenetic Analysis by Maximum
Likelihood (PAML).

PR:		19753
Submitted by:	David A. Bader 
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