65c2 FreshPorts -- biology/dotter
FreshPorts -- The Place For Ports If you buy from Amazon USA, please support us by using this link.
Follow us
Blog
Twitter
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

2860
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
otrsMay 23
otrsMay 23
otrsMay 23
otrsMay 23
chromiumMay 22
chromiumMay 22
firefox*May 21
firefox-devel*May 21
firefox-esr*May 21
firefox10*May 21
firefox15*May 21
firefox3*May 21
firefox3-devel*May 21
firefox35*May 21
firefox36*May 21

8 vulnerabilities affecting 24 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds


Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 24539
Broken 216
Deprecated 487
Ignore 634
Forbidden 2
Restricted 292
No CDROM 109
Vulnerable 25
Expired 123
Set to expire 525
Interactive 33
new 24 hours 8
new 48 hours11
new 7 days36
new fortnight58
new month222

This site
What is FreshPorts?
About the Authors
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact
8e7
Servers and bandwidth provided by
New York Internet, SuperNews, and RootBSD 		Valid HTML, CSS, and RSS.
Copyright © 2000-2013 DVL Software Limited. All rights reserved.
0