The FreeBSD Ports Archive

FreeBSD biology : fasta3

A collection of programs for searching DNA and protein databases

 Version 3 of the FASTA packages contains many programs for searching DNA and
protein databases and one program (prss3) for evaluating statistical
significance from randomly shuffled sequences.  Several additional analysis
programs, including programs that produce local alignments, are available as
part of version 2 of the FASTA package, which is available as the port
biology/fasta.

FASTA is described in:  W. R. Pearson and D. J. Lipman (1988), "Improved
Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R.  Pearson
(1996) "Effective protein sequence comparison" Meth. Enzymol.  266:227-258;
Pearson et. al.  (1997) Genomics 46:24-36;  Pearson, (1999) Meth. in
Molecular Biology 132:185-219.

The FASTA3 suite is distributed freely subject to the condition that it may
not be sold or incorporated into a commercial product.

Author: William R Pearson 
 

fasta3 history

v. 1.21
date: 2007/03/09 11:26:13;  author: miwi;  state: Exp;  lines: +3 -5
- Update to 34.26.2

PR:             110079
Submitted by:   Fernan Aguero (maintainer)

v. 1.20
date: 2006/10/31 09:02:04;  author: miwi;  state: Exp;  lines: +1 -1
- Update to 34.t26.b3

PR:		ports/104508
Submitted by:	Fernan Aguero  (maintainer)

v. 1.19
date: 2006/06/09 19:18:08;  author: pav;  state: Exp;  lines: +2 -2
- Update to 34.t25.d9

PR:		ports/98761
Submitted by:	Fernan Aguero  (maintainer)

v. 1.18
date: 2006/06/05 21:18:23;  author: erwin;  state: Exp;  lines: +2 -2
- Update to 34.t25.d8 [1]
- While I'm here, pet portlint [2]

PR:		98398 [1]
Submitted by:	miwi [1], self [2]
Approved by:	maintainer [1]

v. 1.17
date: 2006/05/24 16:55:46;  author: sem;  state: Exp;  lines: +4 -7
- update to 34.t25.d7
- add MASTER_SITE_LOCAL as a second master site

PR:		ports/97310
Submitted by:	maintainer

v. 1.16
date: 2006/05/21 21:32:08;  author: kris;  state: Exp;  lines: +2 -0
BROKEN: Unfetchable

v. 1.15
date: 2006/05/07 16:52:33;  author: sem;  state: Exp;  lines: +10 -2
- Update to 34.t25.d6

PR:		ports/96063
Submitted by:	maintainer

v. 1.14
date: 2006/03/20 22:23:24;  author: pav;  state: Exp;  lines: +1 -1
- Update to 34.t25.d5

PR:		ports/94741
Submitted by:	Fernan Aguero  (maintainer)

v. 1.13
date: 2006/02/10 09:37:02;  author: lawrance;  state: Exp;  lines: +24 -14
Update to 34.t25.d4.

PR:		ports/93052
Submitted by:	Fernan Aguero  (maintainer)

v. 1.12
date: 2004/07/01 03:02:23;  author: linimon;  state: Exp;  lines: +2 -6
Chase mastersite and fix checksum to unbreak.  (Changes are inclusion of a
logfile, one Linux-only change, and one change in a test script).  Assign
submitter as new maintainer as current one has not responded to PRs for
some time.

PR:		ports/68199
Submitted by:	Fernan Aguero 

v. 1.11
date: 2004/06/21 21:27:11;  author: kris;  state: Exp;  lines: +2 -0
Set an expiry date of 2004-08-20 for these BROKEN/IGNORE/FORBIDDEN
ports.  They will be removed on or after that date if they are still
broken and no fix has been submitted to GNATS.

v. 1.10
date: 2004/02/21 19:31:10;  author: kris;  state: Exp;  lines: +2 -0
BROKEN: Checksum mismatch

v. 1.9
date: 2003/11/15 20:13:21;  author: marcus;  state: Exp;  lines: +1 -1
unPERLify by using REINPLACE_CMD and SED where appropriate.

PR:		47654
Submitted by:	Simon 'portlint' Schubert 

v. 1.8
date: 2003/03/07 05:56:41;  author: ade;  state: Exp;  lines: +2 -1
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

v. 1.7
date: 2001/07/03 09:08:26;  author: wjv;  state: Exp;  lines: +2 -2
Replace erroneous usage of INSTALL_MAN with INSTALL_DATA.

PR:		28666
Submitted by:	Patrick Li 

v. 1.6
date: 2001/06/27 10:14:49;  author: wjv;  state: Exp;  lines: +2 -2
Updating my email address in my remaining ports.

Prompted by:	vanilla

v. 1.5
date: 2001/05/07 12:16:33;  author: jeh;  state: Exp;  lines: +2 -2
Updata biology/fasta3 to version 33.t08.d4

PR:		27176
Submitted by:	Johann Visagie  MAINTAINER

v. 1.4
date: 2001/03/22 09:04:47;  author: sobomax;  state: Exp;  lines: +2 -3
Update to 33.t08.d3.

Submitted by:	maintainer

v. 1.3
date: 2001/03/12 10:24:38;  author: nbm;  state: Exp;  lines: +2 -1
- A small bugfix lead to a rerelease without a version number change.
- Bumped PORTREVISION.

Submitted by:	Johann Visagie 
PR:		25725

v. 1.2
date: 2001/03/08 14:39:07;  author: sf;  state: Exp;  lines: +2 -2
update to 33.t08.d2.

PR:		25609
Submitted by:	maintainer

v. 1.1
date: 2001/02/11 16:28:59;  author: jeh;  state: Exp;
- New port: biology/fasta3, which comprises the FASTA3 suite of DNA and
  protein sequence search programs
- FASTA3 updates only some of the elements of FASTA2, which is why I have
  submitted ports of both versions (as biology/fasta and biology/fasta3)

PR:		24716
Submitted by:	Johann Visagie 
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