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Port details
sim4 Algorithm for aligning expressed DNA with genomic sequences
2003.09.21_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port

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: 27 Jul 2000 11:33:01
License: GPLv2
This package implements the Sim4 algorithm for aligning expressed DNA
with genomic sequences, described in the paper:

L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998)
"A computer program for aligning a cDNA sequence with a genomic DNA sequence."
Genome Research 8, 967-974.

WWW: http://globin.cse.psu.edu/

Port maintained by the FreeBSD bio-porters mailing list.
SVNWeb : Homepage : PortsMon

To install the port: cd /usr/ports/biology/sim4/ && make install clean
To add the package: pkg install sim4

PKGNAME: sim4

distinfo:

SHA256 (sim4.2003-09-21.tar.gz) = 0d65166c1d1951e1d0b83e5d221f23f07462b9d8c46ea0d0569f66e35a5229ee
SIZE (sim4.2003-09-21.tar.gz) = 60814

There are no ports dependent upon this port


Configuration Options
     No options to configure

Master Sites:
  1. http://globin.cse.psu.edu/ftp/dist/sim4/

Number of commits found: 20

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Feb 2014 11:43:07
Original commit files touched by this commit  2003.09.21_1
Revision:344539
ehaupt search for other commits by this committer
Support staging
20 Sep 2013 15:55:44
Original commit files touched by this commit  2003.09.21_1
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)
19 Jun 2013 16:36:53
Original commit files touched by this commit  2003.09.21_1
Revision:321290
bsam search for other commits by this committer
. add license (GPLv2);
. bump PORTREVISION;
. trim article from COMMENT;
. trim Makefile headers.
19 Mar 2011 12:38:54
Original commit files touched by this commit  2003.09.21
miwi search for other commits by this committer
- Get Rid MD5 support
03 May 2006 23:26:35
Original commit files touched by this commit  2003.09.21
edwin search for other commits by this committer
Remove USE_REINPLACE from all categories starting with B
24 Nov 2005 00:04:00
Original commit files touched by this commit  2003.09.21
pav search for other commits by this committer
- Add SHA256
12 Mar 2004 13:53:24
Original commit files touched by this commit  2003.09.21
krion search for other commits by this committer
- Update to version 2003.09.21

PR:             ports/64160
Submitted by:   Liam J. Foy <liamfoy@sepulcrum.org>
05 Feb 2004 20:38:07
Original commit files touched by this commit  2002.03.03
trevor search for other commits by this committer
Use PLIST_FILES.

Reviewed by:    marcus
27 Jan 2004 20:51:07
Original commit files touched by this commit  2002.03.03
trevor search for other commits by this committer
Add SIZE.
02 Nov 2003 02:48:09
Original commit files touched by this commit  2002.03.03
edwin search for other commits by this committer
ports with possibly unreachable MAINTAINERs
*** addresses that seem to be dead:

PR:             ports/58694
Submitted by:   Oliver Eikemeier <eikemeier@fillmore-labs.com>
21 Feb 2003 11:01:38
Original commit files touched by this commit  2002.03.03
knu search for other commits by this committer
De-pkg-comment.
04 May 2002 21:45:10
Original commit files touched by this commit  2002.03.03
kris search for other commits by this committer
Update to sim4-2002.03.03 to unbreak build.

Noticed by:     bento
25 Jan 2002 13:33:01
files touched by this commit
wjv search for other commits by this committer
- Update to version of 2001-12-30    
16 Dec 2001 19:36:48
files touched by this commit
steve search for other commits by this committer
Update to version 2001.10.12.    
19 Feb 2001 12:32:58
files touched by this commit
jeh search for other commits by this committer
Update to version 2001-02-06    
26 Oct 2000 11:19:08
files touched by this commit
jeh search for other commits by this committer
Update biology/sim4 to 2000.10.19   Maintainership over to FreeBSD bio-porters
mailing list    
08 Oct 2000 00:23:30
files touched by this commit
asami search for other commits by this committer
Convert category biology to new layout.  
09 Sep 2000 10:37:15
files touched by this commit
kevlo search for other commits by this committer
Fix checksum    
04 Sep 2000 03:44:04
files touched by this commit
kevlo search for other commits by this committer
Update to version 2000.08.24    
27 Jul 2000 15:33:01
files touched by this commit
nbm search for other commits by this committer
Add sim4, an implementation of the sim4 algorithm for aligning expressed   DNA
with genomic sequences    

Number of commits found: 20

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