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Port details
dotter 20021204 biology Deleted on this many watch lists=0 search for ports that depend on this port
Broken BROKEN: checksum mismatch
Deprecated DEPRECATED: Broken for more than 6 month
Expired This port expired on: 2013-12-18
Ignore IGNORE: is marked as broken: checksum mismatch
Viewer for multiple sequence alignments
Was Maintained by: fbsd-ports@opsec.eu search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:36:50
License: not specified in port


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
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

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

Required To Run:
  1. emulators/linux_base-f10
There are no ports dependent upon this port

No installation instructions: this port has been deleted.

The package name of this deleted port was: dotter


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/dotter-20021204/
  2. ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  3. ftp://ftp.cn.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  4. ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  5. ftp://ftp.ru.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  6. ftp://ftp.se.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  7. ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  8. ftp://ftp.uk.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  9. http://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/
  10. http://sonnhammer.sbc.su.se/download/software/dotter/
Port Moves
  • port moved to biology/seqtools on 2013-11-10
    REASON: Replaced with biology/seqtools

Number of commits found: 19

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
10 Nov 2013 11:01:03
Original commit files touched by this commit  20021204
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>
07 Nov 2013 13:18:51
Original commit files touched by this commit  20021204
Revision:333091
bsam search for other commits by this committer
. 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)
18 Oct 2013 07:19:26
Original commit files touched by this commit  20021204
Revision:330726
bapt search for other commits by this committer
Deprecated some ports broken for more than 6 month
20 Sep 2013 15:55:44
Original commit files touched by this commit  20021204
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
25 Mar 2013 01:41:32
Original commit files touched by this commit  20021204
Revision:315188
miwi search for other commits by this committer
- Mark broken checksum mismatch

Reported by:	pointyhat
http://pointyhat.freebsd.org/errorlogs/i386-errorlogs/a.8.20130324140101.pointyhat/dotter-20021204.log
01 Oct 2012 14:45:17
Original commit files touched by this commit  20021204
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
22 Apr 2011 18:59:11
Original commit files touched by this commit  20021204
glarkin search for other commits by this committer
- 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)
19 Mar 2011 12:38:54
Original commit files touched by this commit  20021204
miwi search for other commits by this committer
- Get Rid MD5 support
28 Apr 2010 22:37:11
Original commit files touched by this commit  20021204
glarkin search for other commits by this committer
- 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)
19 Nov 2009 12:43:06
Original commit files touched by this commit  20021204
miwi search for other commits by this committer
- broken checksum mismatch
16 Sep 2009 15:57:19
Original commit files touched by this commit  20021204
garga search for other commits by this committer
UNBREAK: Probably was a temporary failure, checksums are ok now.

Feature safe:   yes
22 Aug 2009 08:45:12
Original commit files touched by this commit  20021204
miwi search for other commits by this committer
- BROKEN checksum mismatch
17 Aug 2009 15:38:37
Original commit files touched by this commit  20021204
miwi search for other commits by this committer
- Fix fetch

PR:             137840
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
27 Jan 2008 11:26:35
Original commit files touched by this commit  20021204
erwin search for other commits by this committer
Umark BROKEN, stale distfile removed from ftp-master.
25 Jan 2008 20:05:06
Original commit files touched by this commit  20021204
erwin search for other commits by this committer
Mark BROKEN: does not fetch
09 Aug 2007 01:00:45
Original commit files touched by this commit  20021204
kris search for other commits by this committer
Replace IGNORE with ONLY_FOR_ARCHS for this binary port.

Submitted by:   maintainer
03 Aug 2006 20:28:00
Original commit files touched by this commit  20021204
erwin search for other commits by this committer
Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master.
03 Aug 2006 19:06:04
Original commit files touched by this commit  20021204
erwin search for other commits by this committer
Mark BROKEN: checksum mismatch
15 Mar 2006 10:35:24
Original commit files touched by this commit  20021204
garga search for other commits by this committer
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>

Number of commits found: 19

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