| Port details |
- mafft Multiple alignment program for amino acid or nucleotide sequences
- 7.267_1 biology
 =0      7.267Version of this port present on the latest quarterly branch. - Maintainer: cartwright@asu.edu
- Port Added: 2006-03-15 10:41:45
- Last Update: 2024-02-22 13:23:49
- Commit Hash: f5db692
- License: BSD2CLAUSE
- WWW:
- https://mafft.cbrc.jp/alignment/software/
- Description:
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/mafft/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/mafft
- pkg install mafft
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: mafft
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1634878254
SHA256 (mafft-7.267-without-extensions-src.tgz) = 60526e38d3faf3e8d96d9a2e2ecfc9662f0e61c71ed2bc35d07c769703ee86f6
SIZE (mafft-7.267-without-extensions-src.tgz) = 435174
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- ===> The following configuration options are available for mafft-7.267_1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_mafft
- USES:
- gmake shebangfix tar:tgz
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
7.267_1
22 Feb 2024 13:23:49
 |
Muhammad Moinur Rahman (bofh) |
biology/mafft: Moved man to share/man
Approved by: portmgr (blanket) |
7.267
31 Dec 2023 00:37:05
|
Muhammad Moinur Rahman (bofh) |
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
- Remove all references to defunct ARCH arm
- Remove all references to defunct ARCH sparc64
- Remove x11-drivers/xf86-video-sunffb which requires defunct sparc64
ARCH
- Remove sysutils/afbinit requires defunct sparc64 ARCH
- Remove all references to bktr driver
- Remove all references to defunct FreeBSD_12
- Remove all references to OSVERSION/OSREL corresponding to 12
- Remove conditionals in Mk/Uses/cabal.mk
- Remove sparc reference from Mk/Uses/qt-dist.mk
- Remove BROKEN_sparc64/NOT_FOR_ARCH=sparc64
- Remove BROKEN_FreeBSD_12* from:
- Remove OpenSSL patches from:
- Remove conditional flags for OSVERSION >= 1300000 to fixed flags.
Also move conditional flags for non sparc64/arm ARCH to fixed flags.
Reviewed by: brooks, jbeich, rene, salvadore
Differential Revision: https://reviews.freebsd.org/D42068 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
7.267
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
7.267
20 Jul 2022 14:20:57
|
Tobias C. Berner (tcberner) |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
7.267
22 Oct 2021 05:11:23
|
Wen Heping (wen) |
biology/mafft: Update to 7.267
PR: 259315
Reported by: gspurki@gmail.com
Approved by: maintainer |
7.266
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
7.266
19 May 2016 10:21:25
 |
amdmi3 |
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
Approved by: portmgr blanket |
7.266
25 Dec 2015 07:19:00
|
wen |
- Update to 7.266
PR: 205558
Submitted by: cartwright@asu.edu(maintainer) |
7.221
27 Jun 2015 14:30:19
|
bapt |
Use BROKEN helpers |
7.221
03 Jun 2015 17:04:19
|
robak |
biology/mafft: update 7.149 -> 7.221
PR: 200603
Submitted by: Reed A. Cartwright <cartwright@asu.edu> (maintainer) |
7.149
24 Mar 2015 16:01:22
|
marino |
6 ports categories: Remove $PTHREAD_LIBS
Categories: cad, devel, java, x11-fm, biology, deskutils
approved by: PTHREAD blanket |
7.149
20 Oct 2014 07:10:48
|
bapt |
Cleanup plist |
7.149
29 Jul 2014 19:11:53
|
adamw |
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...
Approved by: portmgr (not really, but touches unstaged ports) |
7.149
31 May 2014 04:18:18
|
milki |
Add DOCS and EXAMPLE options to biology/mafft
PR: ports/190161
Submitted by: "Reed A. Cartwright" <cartwright@asu.edu> (maintainer)
Approved by: swills (maintainer) |
7.149
20 May 2014 19:35:30
|
amdmi3 |
- Update to 7.149
- Clarify LICENSE
- Stagify
PR: 189746
Submitted by: "Reed A. Cartwright" <cartwright@asu.edu> (maintainer) |
6.903
13 Mar 2014 07:41:34
|
miwi |
- Convert USE_GMAKE to USES |
6.903
03 Jan 2014 15:46:52
|
adamw |
Convert biology to MDOCS and MEXAMPLES |
6.903
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
6.903
08 Sep 2012 08:30:40
|
linimon |
Mark as broken on sparc64: depends on thread-local storage, which is not
available on sparc64.
Hat: portmgr |
6.903
07 Aug 2012 13:54:02
|
scheidell |
- Submitter is now maintainer
PR: ports/169920
Approved by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) |
6.903
07 Aug 2012 12:26:39
|
scheidell |
- Update to version 6.903
PR: ports/169920
Submitted by: "Reed A. Cartwright" <cartwright@asu.edu>
Approved by: maintainer (timeout, 21 days) |
5.743
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
5.743
27 Jan 2011 17:26:45
|
pav |
- Change depobj for fasta3 to something that does not change on fasta updates
Reported by: pointyhat
Feature safe: yes |
5.743
04 Feb 2009 03:31:00
|
pgollucci |
- Update download locations, update WWW
Reported by: -fetch-original pointyhat run |
5.743
01 Apr 2008 22:24:51
|
pav |
- Chase fasta3 update
Reported by: pointyhat |
5.743
19 Mar 2006 12:59:16
|
garga |
- 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 |
5.734
15 Mar 2006 10:41:16
|
garga |
Add mafft 5.734, multiple sequence alignments based on fast Fourier
transform.
PR: ports/93059
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> |
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