| Port details |
- dotter Viewer for multiple sequence alignments
- 20021204 biology
 =0      20021204Version of this port present on the latest quarterly branch.  BROKEN: checksum mismatch
 DEPRECATED: Broken for more than 6 month
 This port expired on: 2013-12-18
 IGNORE: is marked as broken: checksum mismatch
- Maintainer: fbsd-ports@opsec.eu
- Port Added: 2006-03-15 10:36:50
- Last Update: 2013-11-10 11:01:03
- SVN Revision: 333374
- License: not specified in port
- WWW:
- http://sonnhammer.sbc.su.se/Dotter.html
- Description:
- Dotter is a graphical dotplot program for detailed comparison of
two sequences. Here, every residue in one sequence is compared to
every residue in the other sequence. The first sequence runs along
the x-axis and the second sequence along the y-axis. In regions
where the two sequences are similar to each other, a row of high
scores will run diagonally across the dot matrix. If you're comparing
a sequence against itself to find internal repeats, you'll notice
that the main diagonal scores maximally, since it's the 100% perfect
self-match.
To make the score matrix more intelligible, the pairwise scores are
averaged over a sliding window which runs diagonally. The averaged
score matrix forms a three-dimensional landscape, with the two
sequences in two dimensions and the height of the peaks in the
third. This landscape is projected onto two dimensions by aid of
greyscales - the darker grey of a peak, the higher it is.
Dotter provides a tool to explore the visual appearance of this
landscape, as well as a tool to examine the sequence alignment it
represents.
WWW: http://sonnhammer.sbc.su.se/Dotter.html
 cgit ¦ GitHub ¦ GitHub ¦ GitLab ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- No installation instructions:
- This port has been deleted.
- PKGNAME: dotter
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: i386
- distinfo:
- There is no distinfo for this port.
No package information for this port in our database- Sometimes this happens. Not all ports have packages. Perhaps there is a build error. Check the fallout link:
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Runtime dependencies:
-
- fedora-release : emulators/linux_base-f10
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- N/A
- 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 |
|---|
20021204
10 Nov 2013 11:01:03
  |
wg |
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> |
20021204
07 Nov 2013 13:18:51
|
bsam |
. give maintainership to the submitter;
. add one month to DEPRACATION_DATE;
while here: strip the indefinite article from COMMENT.
PR: ports/183742
Submitted by: Kurt Jaeger <fbsd-ports@opsec.eu> (assigned maintainer) |
20021204
18 Oct 2013 07:19:26
|
bapt |
Deprecated some ports broken for more than 6 month |
20021204
20 Sep 2013 15:55:44
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
20021204
25 Mar 2013 01:41:32
|
miwi |
- Mark broken checksum mismatch
Reported by: pointyhat
http://pointyhat.freebsd.org/errorlogs/i386-errorlogs/a.8.20130324140101.pointyhat/dotter-20021204.log |
20021204
01 Oct 2012 14:45:17
|
tabthorpe |
- Reassign to the heap at maintainer's request |
20021204
22 Apr 2011 18:59:11
|
glarkin |
- Updated WWW: to a working link
- Copied unbranded distfile (dotter.LIN) to LOCAL/glarkin for mirroring to
MASTER_SITE_LOCAL and prevention of fetch checksum error. [1]
Reported by: pointyhat (via miwi) |
20021204
19 Mar 2011 12:38:54
|
miwi |
- Get Rid MD5 support |
20021204
28 Apr 2010 22:37:11
|
glarkin |
- Removed BROKEN because file fetches and checksums correctly
- Added another MASTER_SITES for redundancy
PR: ports/144733
Submitted by: Fernan Aguero <fernan.aguero@gmail.com> (maintainer) |
20021204
19 Nov 2009 12:43:06
|
miwi |
- broken checksum mismatch |
20021204
16 Sep 2009 15:57:19
|
garga |
UNBREAK: Probably was a temporary failure, checksums are ok now.
Feature safe: yes |
20021204
22 Aug 2009 08:45:12
|
miwi |
- BROKEN checksum mismatch |
20021204
17 Aug 2009 15:38:37
|
miwi |
- Fix fetch
PR: 137840
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer) |
20021204
27 Jan 2008 11:26:35
|
erwin |
Umark BROKEN, stale distfile removed from ftp-master. |
20021204
25 Jan 2008 20:05:06
|
erwin |
Mark BROKEN: does not fetch |
20021204
09 Aug 2007 01:00:45
|
kris |
Replace IGNORE with ONLY_FOR_ARCHS for this binary port.
Submitted by: maintainer |
20021204
03 Aug 2006 20:28:00
|
erwin |
Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master. |
20021204
03 Aug 2006 19:06:04
|
erwin |
Mark BROKEN: checksum mismatch |
20021204
15 Mar 2006 10:35:24
|
garga |
Add dotter 20021204 # last modified date in FTP server, a viewer for
multiple sequence alignments.
PR: ports/93055
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> |
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