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Port details
muscle MUltiple Sequence Comparison by Log-Expectation
3.8.1551 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.8.1551Version of this port present on the latest quarterly branch.
Maintainer: mzaki@e-mail.ne.jp search for ports maintained by this maintainer
Port Added: 2008-05-14 13:52:50
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/muscle
  2. /usr/local/share/licenses/muscle-3.8.1551/catalog.mk
  3. /usr/local/share/licenses/muscle-3.8.1551/LICENSE
  4. /usr/local/share/licenses/muscle-3.8.1551/PD
Collapse this list.
Dependency lines:
  • muscle>0:biology/muscle
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):
muscle
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest3.8.15513.8.15513.8.15513.8.15513.8.1551-3.8.1551-
FreeBSD:13:quarterly3.8.15513.8.15513.8.15513.8.15513.8.15513.8.15513.8.15513.8.1551
FreeBSD:14:latest3.8.15513.8.15513.8.15513.8.15513.8.15513.8.1551-3.8.1551
FreeBSD:14:quarterly3.8.15513.8.1551-3.8.15513.8.15513.8.15513.8.15513.8.1551
FreeBSD:15:latest3.8.15513.8.1551n/a3.8.1551n/a3.8.15513.8.15513.8.1551
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. http://www.drive5.com/muscle/
Collapse this list.

Number of commits found: 18

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
3.8.1551
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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 View all of this commit message)
3.8.1551
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
3.8.1551
17 Jan 2020 16:49:03
Revision:523339Original commit files touched by this commit
fernape search for other commits by this committer
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
Revision:522911Original commit files touched by this commit
fernape search for other commits by this committer
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
Revision:425879Original commit files touched by this commit
linimon search for other commits by this committer
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
Revision:403676Original commit files touched by this commit
swills search for other commits by this committer
mark some of the ports that don't build on powerpc64 for me
3.8.31
17 Jun 2014 21:36:06
Revision:358182Original commit files touched by this commit
rakuco search for other commits by this committer
Update to 3.8.31.

PR:		191130
Submitted by:	mzaki@m.u-tokyo.ac.jp (maintainer)
3.6
01 Jun 2014 11:05:44
Revision:356095Original commit files touched by this commit
ohauer search for other commits by this committer
- add stage support
3.6
26 May 2014 06:55:07
Revision:355278Original commit files touched by this commit
bapt search for other commits by this committer
Convert to USES=dos2unix

With hat:	portmgr
3.6
13 Mar 2014 07:41:34
Revision:348042Original commit files touched by this commit
miwi search for other commits by this committer
- Convert USE_GMAKE to USES
3.6
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
3.6
24 Jul 2012 07:19:21
Original commit files touched by this commit
cs search for other commits by this committer
Fix typos in COMMENT
3.6
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
3.6
17 May 2008 16:52:34
Original commit files touched by this commit
pav search for other commits by this committer
- Update maintainer's email address

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
3.6
17 May 2008 16:50:12
Original commit files touched by this commit
pav search for other commits by this committer
- Try to fix fetch

Submitted by:   Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> (maintainer)
3.6
14 May 2008 13:51:50
Original commit files touched by this commit
pav search for other commits by this committer
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>

Number of commits found: 18