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Port details
mafft Multiple alignment program for amino acid or nucleotide sequences
7.149 biology on this many watch lists=0 search for ports that depend on this port
Maintained by: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:41:45
License: BSD2CLAUSE
MAFFT offers a range of multiple alignment strategies, L-INS-i
(accurate; recommended for <200 sequences), FFT-NS-i (standard speed and
accuracy), FFT-NS-2 (fast; recommended for >2,000 sequences), etc.
According to BAliBASE and other benchmark tests, L-INS-i is one of the
most accurate methods currently available.

MAFFT has been described:

K. Katoh and H. Toh 2008 (Briefings in Bioinformatics 9:286-298)
Recent developments in the MAFFT multiple sequence alignment program.

K. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30:
3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence
alignment based on fast Fourier transform. 

WWW: http://mafft.cbrc.jp/alignment/software/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Required To Build:
  1. devel/gmake
There are no ports dependent upon this port

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


Configuration Options
===> The following configuration options are available for mafft-7.149:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

Master Sites:
  1. http://distcache.FreeBSD.org/ports-distfiles/
  2. http://mafft.cbrc.jp/alignment/software/

Number of commits found: 16

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
20 Oct 2014 07:10:48
Original commit files touched by this commit  7.149
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  7.149
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)
31 May 2014 04:18:18
Original commit files touched by this commit  7.149
Revision:355931
milki search for other commits by this committer
Add DOCS and EXAMPLE options to biology/mafft

PR:		ports/190161
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu> (maintainer)
Approved by:	swills (maintainer)
20 May 2014 19:35:30
Original commit files touched by this commit  7.149
Revision:354673
amdmi3 search for other commits by this committer
- Update to 7.149
- Clarify LICENSE
- Stagify

PR:		189746
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu> (maintainer)
13 Mar 2014 07:41:34
Original commit files touched by this commit  6.903
Revision:348042
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
03 Jan 2014 15:46:52
Original commit files touched by this commit  6.903
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  6.903
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)
08 Sep 2012 08:30:40
Original commit files touched by this commit  6.903
Revision:303880
linimon search for other commits by this committer
Mark as broken on sparc64: depends on thread-local storage, which is not
available on sparc64.

Hat:		portmgr
07 Aug 2012 13:54:02
Original commit files touched by this commit  6.903
scheidell search for other commits by this committer
- Submitter is now maintainer

PR:		ports/169920
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
07 Aug 2012 12:26:39
Original commit files touched by this commit  6.903
scheidell search for other commits by this committer
- Update to version 6.903

PR:		ports/169920
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu>
Approved by:	maintainer (timeout, 21 days)
19 Mar 2011 12:38:54
Original commit files touched by this commit  5.743
miwi search for other commits by this committer
- Get Rid MD5 support
27 Jan 2011 17:26:45
Original commit files touched by this commit  5.743
pav search for other commits by this committer
- Change depobj for fasta3 to something that does not change on fasta updates

Reported by:    pointyhat
Feature safe:   yes
04 Feb 2009 03:31:00
Original commit files touched by this commit  5.743
pgollucci search for other commits by this committer
- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run
01 Apr 2008 22:24:51
Original commit files touched by this commit  5.743
pav search for other commits by this committer
- Chase fasta3 update

Reported by:    pointyhat
19 Mar 2006 12:59:16
Original commit files touched by this commit  5.743
garga search for other commits by this committer
- Update to 5.743
- Add a MASTER_SITE backup since oficial one just have last version and make
  it fetchable again

Submitted by:   maintainer by email
Reported by:    krismail
15 Mar 2006 10:41:16
Original commit files touched by this commit  5.734
garga search for other commits by this committer
Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.

PR:             ports/93059
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

Number of commits found: 16

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