4358 FreshPorts -- biology/mafft
FreshPorts -- The Place For Ports If you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter

Port details
mafft 6.903 biology on this many watch lists=0 search for ports that depend on this port
Multiple alignment program for amino acid or nucleotide sequences
Maintained by: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:41:45
License: BSD


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 required dependencies information. Optional dependencies are not covered.

Required To Build:
  1. devel/gmake
Required To Run:
  1. biology/fasta3
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_add -r mafft


Configuration Options
     No options to configure

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

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
08 Sep 2012 08:30:40
Original commit files touched by this commit  6.903
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: 9

28af
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
asterisk*Jun 19
asterisk10*Jun 19
clamav*Jun 19
clamav-devel*Jun 19
cyrus-imspd*Jun 19
glpi*Jun 19
otrsJun 19
otrsJun 19
tshark*Jun 19
tshark-lite*Jun 19
wireshark*Jun 19
wireshark-lite*Jun 19
apache-xml-security-cJun 18
linux-f10-flashplugin10*Jun 18
linux-f10-flashplugin11*Jun 18

15 vulnerabilities affecting 24 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds


Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 24572
Broken 187
Deprecated 454
Ignore 561
Forbidden 0
Restricted 288
No CDROM 110
Vulnerable 19
Expired 48
Set to expire 439
Interactive 33
new 24 hours 6
new 48 hours13
new 7 days33
new fortnight84
new month177

This site
What is FreshPorts?
About the Authors
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact
8e7

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2013 DVL Software Limited. All rights reserved.
0