65c2 FreshPorts -- biology/dotter
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Port details
dotter 20021204 biology on this many watch lists=0 search for ports that depend on this port
Broken BROKEN: checksum mismatch
Ignore IGNORE: is marked as broken: checksum mismatch
A viewer for multiple sequence alignments

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org 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

To install the port: cd /usr/ports/biology/dotter/ && make install clean

A package is not available for ports marked as: Forbidden / Broken / Ignore / Restricted

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/

Number of commits found: 15

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
25 Mar 2013 01:41:32
Original commit files touched by this commit  20021204
 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
 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: 15

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