dotter 20021204 biology =0

IGNORE: is only for i386, while you are running amd64
A viewer for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar
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

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required To Run: emulators/linux_base-f10
There are no ports dependent upon this port

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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

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Configuration Options

     No options to configure

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Master Sites:

http://sonnhammer.sbc.su.se/download/software/dotter/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.se.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.uk.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.ru.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.jp.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.tw.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.cn.FreeBSD.org/pub/FreeBSD/ports/local-distfiles/glarkin/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/dotter-20021204/

- 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)

- Get Rid MD5 support

- 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)

- broken checksum mismatch

UNBREAK: Probably was a temporary failure, checksums are ok now.

Feature safe:   yes

- BROKEN checksum mismatch

- Fix fetch

PR:             137840
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

Umark BROKEN, stale distfile removed from ftp-master.

Mark BROKEN: does not fetch

Replace IGNORE with ONLY_FOR_ARCHS for this binary port.

Submitted by:   maintainer

Unmark BROKEN, it seems to be caused by a stale distfile on ftp-master.

Mark BROKEN: checksum mismatch

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>

15 vulnerabilities affecting 34 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities