FreshPorts -- The Place For Ports If you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter

non port: head/biology/seqtools/distinfo
SVNWeb

Number of commits found: 25

Fri, 11 Nov 2016
[ 06:19 pi ] Original commit   Revision:425863
425863 biology/seqtools/Makefile
425863 biology/seqtools/distinfo
425863 biology/seqtools/files
425863 biology/seqtools/files/patch-gbtools_src_blatSrc_lib_gff3.c
biology/seqtools: update 4.43.0 -> 4.44.1

- Blixem: Features can now be added to multiple different groups/filters.
- Belvu: Fix a problem where column highlighting can get out of sync
  with the text.
Sun, 31 Jul 2016
[ 14:19 pi ] Original commit   Revision:419380
419380 biology/seqtools/Makefile
419380 biology/seqtools/distinfo
419380 biology/seqtools/pkg-plist
biology/seqtools: 4.42.1 -> 4.43.0

 
ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/release_notes.html

- Mark broken on 9.x: Fails to build due to C++ std issues
Fri, 22 Apr 2016
[ 16:27 pi ] Original commit   Revision:413787
413787 biology/seqtools/Makefile
413787 biology/seqtools/distinfo
biology/seqtools: 4.41.1 -> 4.42.1

- fixes build on 9.x
- Added a feedback box to show the read depth at the selected coord.
  Hover over this box to see the specific base support (i.e. the
  number of A/C/G/Ts).
Mon, 14 Mar 2016
[ 19:40 pi ] Original commit   Revision:411109
411109 biology/seqtools/Makefile
411109 biology/seqtools/distinfo
411109 biology/seqtools/pkg-plist
biology/seqtools: 4.40.0 -> 4.41.1

- mostly internal changes, some build fixes
Sat, 6 Feb 2016
[ 10:17 pi ] Original commit   Revision:408287
408287 biology/seqtools/Makefile
408287 biology/seqtools/distinfo
biology/seqtools: 4.39.3 -> 4.40.0

- Blixem can now accept a 'command' tag in a gff line for a region
  feature. The given command should return gff and will be run by
  blixem on the given region.
- Blixem now supports fetching sequence data over https.
Sat, 5 Dec 2015
[ 13:20 pi ] Original commit   Revision:403064
403064 biology/seqtools/Makefile
403064 biology/seqtools/distinfo
biology/seqtools: 4.39.2 -> 4.39.3

- Blixem
  Further improve the display of features in the detail view
  when they have transparent fill, making sure that they have a
  visible border.
Tue, 1 Dec 2015
[ 20:50 pi ] Original commit   Revision:402787
402787 biology/seqtools/Makefile
402787 biology/seqtools/distinfo
biology/seqtools: 4.39.1 -> 4.39.2

- Blixem:
  Improve the display of features in the detail view when they
  have transparent fill.
Wed, 18 Nov 2015
[ 10:53 pi ] Original commit   Revision:401862
401862 biology/seqtools/distinfo
401862 biology/seqtools/pkg-descr
biology/seqtools: Fix distinfo, WWW

- Side effect of the seqtools automated build system

Submitted by:	pkg-fallout
Fri, 13 Nov 2015
[ 18:46 pi ] Original commit   Revision:401527
401527 biology/seqtools/Makefile
401527 biology/seqtools/distinfo
biology/seqtools: 4.39.0 -> 4.39.1

- Fix a bug in Belvu where the display was being initialised in
  command-line-only modes.
Sun, 8 Nov 2015
[ 16:39 pi ] Original commit   Revision:401065
401065 biology/seqtools/Makefile
401065 biology/seqtools/distinfo
biology/seqtools: 4.36 -> 4.39.0

- Blixem
  o There is now an optional setting to highlight "maybe-canonical"
    splice sites in Blixem. This can be used to help identify
    problems where the strand is incorrect in the input data - it
    highlights splice sites in a different colour if they would be
    canonical were they on the other strand.
  o Fixed a bug with colinearity lines when an alignment's cigar
    string contains introns.
  o There are now separate feedback boxes for the selected sequence
    name coordinates. Hover over each box to see a tooltip describing
    its contents.
Sat, 8 Aug 2015
[ 11:22 pi ] Original commit   Revision:393723
393723 biology/seqtools/Makefile
393723 biology/seqtools/distinfo
biology/seqtools: 4.35 -> 4.36

Minor under-the-hood changes
Tue, 7 Jul 2015
[ 14:17 pi ] Original commit   Revision:391503
391503 biology/seqtools/Makefile
391503 biology/seqtools/distinfo
biology/seqtools: 4.34.1 -> 4.35

- Blixem bug fix in sorting features, RT 473624
- Compilation of the seqtools in parallel, RT 467905
- Fix bug with sorting by similarity/identity to first sequence (RT:473624)
- Fix an error compiling with multiple threads (RT:467905)
Wed, 6 May 2015
[ 20:30 pi ] Original commit   Revision:385561
385561 biology/seqtools/Makefile
385561 biology/seqtools/distinfo
385561 biology/seqtools/pkg-plist
biology/seqtools: 4.33 -> 4.34.1

Blixem
- Added functionality to shift-select a range of coordinates,
  and copy the reference/match sequence for that range.
- DNA search now highlights the resultant range of coordinates.
- Added a splitter bar to allow the variations track to be resized.
- Dotter
  Fix a crash pressing Esc on an undocked alignment or greyramp tool.
- All
  Code reorganisation: the codebase is now in C++ rather than C,
  and a new module 'gbtools' has been created for generic
  utility functions.
Tue, 31 Mar 2015
[ 18:04 pi ] Original commit   Revision:382855
382855 biology/seqtools/Makefile
382855 biology/seqtools/distinfo
biology/seqtools: 4.32 -> 4.33

- Blixem/Dotter
  Multi-dotter support; may now start multiple dotters from blixem
Thu, 12 Feb 2015
[ 12:04 pi ] Original commit   Revision:378870
378870 biology/seqtools/Makefile
378870 biology/seqtools/distinfo
biology/seqtools: 4.31 -> 4.32

- Blixem
  o Previously-unsupported GFF feature types can now be displayed
    as a new 'basic feature' type.
  o Styles are now applied to the detail view as well as the big
    picture, so feature display is more consistent across the two
    views.
  o Fix a bug where styles were not being applied to
    dynamically-loaded features.
- Dotter
  o Added a 'maximise' button for the greyramp tool.
  o Small fixes to inconsistencies in context-sensitive menus and
    keyboard shortcuts.
Sat, 13 Dec 2014
[ 18:10 pi ] Original commit   Revision:374668
374668 biology/seqtools/Makefile
374668 biology/seqtools/distinfo
biology/seqtools: 4.30 -> 4.31

Some changes to sqlite dependencies
Tue, 4 Nov 2014
[ 13:19 pi ] Original commit   Revision:372142
372142 biology/seqtools/Makefile
372142 biology/seqtools/distinfo
biology/seqtools: 4.29 -> 4.30

- Blixem
  o Fix potential crash with internal processing
  o Fix two bugs in data input
Wed, 15 Oct 2014
[ 18:46 pi ] Original commit   Revision:370943
370943 biology/seqtools/Makefile
370943 biology/seqtools/distinfo
370943 biology/seqtools/pkg-plist
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.
Thu, 31 Jul 2014
[ 03:17 pi ] Original commit   Revision:363530
363530 biology/seqtools/Makefile
363530 biology/seqtools/distinfo
biology/seqtools: 4.27 -> 4.28
Sat, 12 Jul 2014
[ 18:56 pi ] Original commit   Revision:361635
361635 biology/seqtools/Makefile
361635 biology/seqtools/distinfo
biology/seqtools: 4.26 -> 4.27
Fri, 2 May 2014
[ 19:00 pi ] Original commit   Revision:352838
352838 biology/seqtools/Makefile
352838 biology/seqtools/distinfo
biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgrading

Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
Thu, 1 May 2014
[ 16:50 pi ] Original commit   Revision:352761
352761 biology/seqtools/Makefile
352761 biology/seqtools/distinfo
biology/seqtools: 4.24 -> 4.25

PR:             ports/186299
Submitted by:   pi (myself)
Approved by:    jadawin (mentor)
Tue, 24 Dec 2013
[ 17:23 wg ] Original commit   Revision:337375
337375 biology/seqtools/Makefile
337375 biology/seqtools/distinfo
biology/seqtools: update to 4.24

PR:		ports/185162
Submitted by:	maintainer
Thu, 14 Nov 2013
[ 20:09 wg ] Original commit   Revision:333786
333786 biology/seqtools/Makefile
333786 biology/seqtools/distinfo
biology/seqtools: update to 4.23

PR:		ports/183960
Submitted by:	maintainer
Sun, 10 Nov 2013
[ 11:01 wg ] Original commit   Revision:333374
333374 MOVED
333374 biology/Makefile
333374 biology/dotter
333374 biology/seqtools
333374 biology/seqtools/Makefile
333374 biology/seqtools/distinfo
333374 biology/seqtools/pkg-descr
333374 biology/seqtools/pkg-plist
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: 25

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
apache24Dec 06
cryptoppDec 06
mod_http2-develDec 06
py-cryptography*Dec 06
qemu*Dec 06
qemu-devel*Dec 06
qemu-sbruno*Dec 06
chromiumDec 05
ImageMagickDec 04
ImageMagick-nox11Dec 04
ImageMagick7Dec 04
ImageMagick7Dec 04
ImageMagick7-nox11Dec 04
ImageMagick7-nox11Dec 04
py-pillowDec 04

35 vulnerabilities affecting 74 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 26963
Broken 313
Deprecated 177
Ignore 577
Forbidden 1
Restricted 214
No CDROM 82
Vulnerable 59
Expired 9
Set to expire 156
Interactive 0
new 24 hours 24
new 48 hours31
new 7 days80
new fortnight122
new month294

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2014 Dan Langille. All rights reserved.