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Port details
seqtools Tools for visualising sequence alignments
4.31 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
Maintainer: pi@FreeBSD.org search for ports maintained by this maintainer
Port Added: 10 Nov 2013 11:01:14
License: GPLv3
A suite of tools for visualising sequence alignments.

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.
It has an extensive set of user-configurable modes to color residues
by conservation or by residue type, and some basic alignment editing
capabilities.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences. Every residue in one sequence is compared to every
residue in the other, with one sequence plotted on the x-axis and
the other on the y-axis.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/
SVNWeb : Homepage : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. pkgconf : devel/pkgconf
  2. /usr/local/bin/intltool-extract : textproc/intltool
Library dependencies:
  1. libcurl.so : ftp/curl
  2. libsqlite3.so : databases/sqlite3
  3. libexecinfo.so : devel/libexecinfo
  4. libatk-1.0.so : accessibility/atk
  5. libglib-2.0.so : devel/glib20
  6. libgtk-x11-2.0.so : x11-toolkits/gtk20
  7. libpango-1.0.so : x11-toolkits/pango
There are no ports dependent upon this port

To install the port: cd /usr/ports/biology/seqtools/ && make install clean
To add the package: pkg install biology/seqtools


Configuration Options
===> The following configuration options are available for seqtools-4.31:
     DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings

Master Sites:
  1. ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/
  2. http://distcache.FreeBSD.org/ports-distfiles/
Port Moves
  • port moved here from biology/dotter on 2013-11-10
    REASON: Replaced with biology/seqtools

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
13 Dec 2014 18:10:32
Original commit files touched by this commit  4.31
Revision:374668
pi search for other commits by this committer
biology/seqtools: 4.30 -> 4.31

Some changes to sqlite dependencies
04 Nov 2014 13:19:24
Original commit files touched by this commit  4.30
Revision:372142
pi search for other commits by this committer
biology/seqtools: 4.29 -> 4.30

- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input
15 Oct 2014 18:46:06
Original commit files touched by this commit  4.29
Revision:370943
pi search for other commits by this committer
biology/seqtools: 4.28 -> 4.29

- Blixem
  o Added the facility to run Dotter on an ad-hoc sequence (RT:408836).
  o Added the facility to run Dotter against a transcript.
- Dotter
  Minimise the greyramp tool to a simple contrast slider. Use
  Ctrl-G to toggle between this and the full greyramp tool.
- Belvu
  Fix a bug with tree bootstrapping in Belvu.
04 Aug 2014 23:06:21
Original commit files touched by this commit  4.28
Revision:364067
bapt search for other commits by this committer
USES=execinfo
31 Jul 2014 03:17:55
Original commit files touched by this commit  4.28
Revision:363530
pi search for other commits by this committer
biology/seqtools: 4.27 -> 4.28
15 Jul 2014 23:11:13
Original commit files touched by this commit  4.27
Revision:362014
adamw search for other commits by this committer
Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.

Where possible, correct a few instances where PORTDOCS was being used
to flag stuff in EXAMPLESDIR. For some ports, mostly those owned by
ruby@, PORTDOCS is applied to pretty much everything whether it's
documentation or example.
12 Jul 2014 18:56:04
Original commit files touched by this commit  4.27
Revision:361635
pi search for other commits by this committer
biology/seqtools: 4.26 -> 4.27
27 Jun 2014 17:21:07
Original commit files touched by this commit  4.26_1
Revision:359586
miwi search for other commits by this committer
- Chase database/sqlite3 slib bump

Approved by:	portmgr (myself)
08 Jun 2014 19:51:28
Original commit files touched by this commit  4.26
Revision:357070
olgeni search for other commits by this committer
Remove all space characters from Makefile assignments.

No functional changes included.

CR:		D193 (except math/sedumi)
Approved by:	portmgr (bapt)
02 May 2014 19:00:05
Original commit files touched by this commit  4.26
Revision:352838
pi search for other commits by this committer
biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading

Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
01 May 2014 16:50:34
Original commit files touched by this commit  4.25
Revision:352761
pi search for other commits by this committer
biology/seqtools: 4.24 -> 4.25

PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
12 Feb 2014 14:03:25
Original commit files touched by this commit  4.24_1
Revision:343923
mat search for other commits by this committer
Fix old makeplist bug.

Pointy hat to:	people who blindly use makeplist
Sponsored by:	Absolight
24 Dec 2013 17:23:23
Original commit files touched by this commit  4.24
Revision:337375
wg search for other commits by this committer
biology/seqtools: update to 4.24

PR:		ports/185162
Submitted by:	maintainer
14 Nov 2013 20:09:01
Original commit files touched by this commit  4.23
Revision:333786
wg search for other commits by this committer
biology/seqtools: update to 4.23

PR:		ports/183960
Submitted by:	maintainer
10 Nov 2013 11:01:03
Original commit files touched by this commit  4.22
Revision:333374
wg search for other commits by this committer
biology/seqtools: Tools for visualising sequence alignments

Blixem is an interactive browser of pairwise alignments that have
been stacked up in a "master-slave" multiple alignment; it is not
a 'true' multiple alignment but a 'one-to-many' alignment.

Belvu is a multiple sequence alignment viewer and phylogenetic tool.

Dotter is a graphical dot-matrix program for detailed comparison
of two sequences.

WWW: http://www.sanger.ac.uk/resources/software/seqtools/

PR:		ports/183801
Submitted by:	Kurt Jaeger <fbsd-ports opsec.eu>

Number of commits found: 15

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