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.
===> 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
*/*: 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
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)
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 )
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 )
Add DOCS and EXAMPLE options to biology/mafft
PR: ports/190161
Submitted by: "Reed A. Cartwright" <cartwright@asu.edu> (maintainer)
Approved by: swills (maintainer)
- 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
