The FreeBSD Ports Archive

FreeBSD biology : t_coffee

A multiple DNA or protein sequence alignment package

 From the website:

  T-Coffee is a multiple sequence alignment package. Given a set of sequences
  (Proteins or DNA), T-Coffee generates a multiple sequence alignment.

  Related publications:
  - 3DCoffee: Combining Protein Sequences and Structures within Multiple
    Sequence Alignments.
    O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins, C. Notredame.
    Journal of Molecular Biology, Vol 340, pp385-395, 2004
  - T-Coffee: A novel method for multiple sequence alignments.  C.Notredame,
    D. Higgins, J. Heringa, Journal of Molecular Biology,Vol 302,
    pp205-217,2000
  - COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
    C.  Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14 (5)
    407-422,1998

Author: Cedric Notredame 
 

t_coffee history

v. 1.14
date: 2007/05/02 07:15:46;  author: edwin;  state: Exp;  lines: +2 -7
[patch] cleanup non-supported FreeBSD versions

PR:		ports/111728
Submitted by:	Edwin Groothuis 
Approved by:	maintainer timeout

v. 1.13
date: 2007/03/09 11:26:16;  author: miwi;  state: Exp;  lines: +1 -1
- Update to 4.96

PR:             110080
Submitted by:   Fernan Aguero (maintainer)

v. 1.12
date: 2007/01/22 23:22:53;  author: rafan;  state: Exp;  lines: +1 -1
- Project moves to a new home. Change MASTER_SITES and WWW

PR:		ports/108214
Submitted by:	Thomas Abthorpe 
Approved by:	Fernan Aguero  (maintainer)

v. 1.11
date: 2006/02/10 09:45:28;  author: lawrance;  state: Exp;  lines: +7 -7
Update to 3.27.
Use GCC 3.3 on systems with 3.4, due to an internal compiler error.

PR:		ports/93050
Submitted by:	Fernan Aguero  (maintainer)

v. 1.10
date: 2005/12/06 15:10:08;  author: tdb;  state: Exp;  lines: +8 -4
- Update to 3.18 to make fetchable again
- Mark broken on 6.x upwards

PR:		89977
Submitted by:	Fernan Aguero  (maintainer)
Approved by:	clement (mentor)

v. 1.9
date: 2005/10/28 06:32:18;  author: kris;  state: Exp;  lines: +2 -0
BROKEN: Unfetchable

v. 1.8
date: 2005/10/11 20:47:02;  author: sem;  state: Exp;  lines: +0 -0
Forced commit to note the port was updated to 3.14 not 3.13

v. 1.7
date: 2005/10/11 20:44:38;  author: sem;  state: Exp;  lines: +6 -8
- Update to 3.13. It fixes fetching.

PR:		ports/87264
Submitted by:	maintainer

v. 1.6
date: 2004/11/25 23:03:54;  author: sem;  state: Exp;  lines: +13 -25
- Update to 2.03
- Pass maintainership to submitter

PR:		ports/74332
Submitted by:	Fernan Aguero 

v. 1.5
date: 2004/11/20 08:09:45;  author: linimon;  state: Exp;  lines: +1 -1
With portmgr hat on, reset inactive maintainer.  These ports are now up
for adoption.

v. 1.4
date: 2004/01/22 12:18:01;  author: trevor;  state: Exp;  lines: +1 -1
Use the CPIO macro defined in bsd.port.mk.

v. 1.3
date: 2003/11/13 14:44:58;  author: trevor;  state: Exp;  lines: +1 -1
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.

v. 1.2
date: 2003/03/07 05:56:43;  author: ade;  state: Exp;  lines: +1 -0
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

v. 1.1
date: 2002/01/25 14:58:14;  author: wjv;  state: Exp;
Add t_coffee 1.37, a multiple DNA or protein sequence alignment package.
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