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Port details
dotter 20021204 biology on this many watch lists=0 search for ports that depend on this port
Ignore IGNORE: is only for i386, while you are running amd64
A viewer for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 15 Mar 2006 10:36:50


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://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon
Required To Run: emulators/linux_base-fc4

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:
ftp://ftp.cgb.ki.se/pub/esr/dotter/
ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/dotter-20021204/

Number of commits found: 6

Commit History - (may be incomplete: see CVSWeb link above for full details)
DateByDescription
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 02:00:45
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 21:28:00
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 20:06:04
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: 6

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