| Port details |
- muscle MUltiple Sequence Comparison by Log-Expectation
- 3.8.1551 biology
 =2      3.8.1551Version of this port present on the latest quarterly branch. - Maintainer: mzaki@e-mail.ne.jp
- Port Added: 2008-05-14 13:52:50
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: PD
- WWW:
- https://www.drive5.com/muscle/
- Description:
- MUSCLE is multiple alignment software for protein and nucleotide sequences.
The name stands for multiple sequence comparison by log-expectation.
A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.
Citation:
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.
The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.
  ¦  ¦  ¦  ¦ 
- 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/muscle/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/muscle
- pkg install muscle
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: muscle
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1578543217
SHA256 (muscle_src_3.8.1551.tar.gz) = c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e
SIZE (muscle_src_3.8.1551.tar.gz) = 190019
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
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_muscle
- USES:
- dos2unix gmake
- 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 |
|---|
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) |
3.8.1551
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  ) |
3.8.1551
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 ) |
3.8.1551
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
3.8.1551
17 Jan 2020 16:49:03
 |
fernape |
biology/muscle: unbreak in -CURRENT
Don't compile problematic (and unnecessary) file.
PR: 243206
Submitted by: mzaki@e-mail.ne.jp (maintainer) |
3.8.1551
13 Jan 2020 17:42:22
|
fernape |
biology/muscle: update to 3.8.1551
* Bug fix for long sequences.
* Unbreak '/dev/tty' problem during a build
* Update maintainer's mail address
PR: 243206
Submitted by: mzaki@e-mail.ne.jp (maintainer) |
3.8.31
11 Nov 2016 09:31:03
|
linimon |
Mark various leaf ports broken on aarch64, and, where appropriate, other
tier-2 archs.
Approved by: portmgr (tier-2 blanket) |
3.8.31
13 Dec 2015 16:07:28
|
swills |
mark some of the ports that don't build on powerpc64 for me |
3.8.31
17 Jun 2014 21:36:06
|
rakuco |
Update to 3.8.31.
PR: 191130
Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) |
3.6
01 Jun 2014 11:05:44
|
ohauer |
- add stage support |
3.6
26 May 2014 06:55:07
|
bapt |
Convert to USES=dos2unix
With hat: portmgr |
3.6
13 Mar 2014 07:41:34
|
miwi |
- Convert USE_GMAKE to USES |
3.6
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
3.6
24 Jul 2012 07:19:21
|
cs |
Fix typos in COMMENT |
3.6
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
3.6
17 May 2008 16:52:34
|
pav |
- Update maintainer's email address
Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) |
3.6
17 May 2008 16:50:12
|
pav |
- Try to fix fetch
Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer) |
3.6
14 May 2008 13:51:50
|
pav |
MUSCLE is multiple alignment software for protein and nucleotide sequences.
The name stands for multiple sequence comparison by log-expectation.
A range of options is provided that give you the choice of optimizing
accuracy, speed, or some compromise between the two. Default parameters are
those that give the best average accuracy in the published tests. MUSCLE
can achieve both better average accuracy and better speed than CLUSTALW or
T-Coffee, depending on the chosen options.
Citation:
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy
and high throughput. Nucleic Acids Research 32(5): 1792-1797.
Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.
The NAR paper gives only a brief overview of the algorithm and
implementation details. For a full discussion of the method and many of
the non-default options that it offers, please see the BMC paper.
WWW: http://www.drive5.com/muscle/
PR: ports/118460
Submitted by: Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> |
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