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5081af2c64
freebsd-ports/biology
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Edwin Groothuis 5081af2c64 New port: biology/consed viewing and editing workbench for sequence 
assembly

	Consed is a tool for viewing, editing, and finishing sequence
	assemblies.

	The port is constituted of 4 parts:
	biology/phred: base caller with quality evaluation
	biology/phrap: sequence assembler for shotgun sequencing
	biology/consed: workbench
	biology/phd2fasta: small utility

	All these can be used separately; however, most function
	of consed depends on the others.

	Although these programs are licensed freely for academic
	and nonprofit purposes, users have to contact the authors
	to get the softwares.
	Phred (including phd2fasta) and phrap are emailed,
	and consed can be downloaded to a restricted IP address.
	For commercial users, the licensing fee is ca. $10,000 at
	the time of writing.

PR:		ports/118548
Submitted by:	Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
2008-05-24 07:04:45 +00:00
..
adun - add PORTSCOUT 2008-05-04 11:41:25 +00:00
ariadne
artemis - Update to version 9 2007-07-08 11:47:58 +00:00
avida [patch] cleanup non-supported FreeBSD versions 2007-05-02 07:13:53 +00:00
babel
belvu
biococoa - update for gnustep-make-2.0.0 2007-05-25 05:55:36 +00:00
biojava - Welcome X.org 7.2 \o/. 2007-05-19 20:36:56 +00:00
blast Remove always-false/true conditions based on OSVERSION 500000 2007-10-04 00:15:01 +00:00
blat Update to version 34. 2008-04-30 23:19:29 +00:00
boinc-simap implement @dirrmtry macro for the pkg-plist 2008-04-19 00:24:21 +00:00
chemeq Migration from bison 1.x to 2.x 2007-10-17 10:13:01 +00:00
clustalw - Update to 2.0.6 2008-04-29 12:58:52 +00:00
consed New port: biology/consed viewing and editing workbench for sequence 2008-05-24 07:00:37 +00:00
crimap - Fix the build with GCC 4.2 2007-06-18 21:35:50 +00:00
distribfold - Remove unreachable OSVERSION code. 2007-04-16 11:57:17 +00:00
dna-qc Remove always-true condition due to OSVERSION 2007-04-16 11:58:10 +00:00
dotter Umark BROKEN, stale distfile removed from ftp-master. 2008-01-27 11:26:35 +00:00
embassy - Update to 5.0.0 2008-04-13 07:22:42 +00:00
emboss - Replace SF with second working master site 2008-04-17 17:06:48 +00:00
fasta - Update mastersite. 2008-04-18 15:36:54 +00:00
fasta3 - Update to 35.3.6 2008-04-10 08:09:10 +00:00
fastdnaml
finchtv
fluctuate
garlic - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
genpak - Welcome X.org 7.2 \o/. 2007-05-19 20:36:56 +00:00
gff2ps Reset chuynh@biolateral.com.au: address bounces. 2007-03-10 20:20:10 +00:00
gmap [patch] cleanup non-supported FreeBSD versions 2007-04-16 21:18:53 +00:00
gperiodic - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
grappa
hmmer
jalview - Welcome X.org 7.2 \o/. 2007-05-19 20:36:56 +00:00
kinemage - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
L-Breeder - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
lagan
lamarc - Update to 2.1.2b 2007-10-23 23:07:19 +00:00
libgenome
linux-foldingathome - Fix typo in WWW 2007-10-04 07:28:40 +00:00
lsysexp - Remove USE_X_PREFIX 2008-03-21 20:00:05 +00:00
mafft - Chase fasta3 update 2008-04-01 22:24:51 +00:00
mapm3 MAPMAKER/EXP is a linkage analysis package designed to help construct primary 2008-04-06 04:49:05 +00:00
migrate - File was rerolled for a small bugfix. 2008-02-27 07:34:21 +00:00
molden - Mark BROKEN on -CURRENT: error: 'linkat' redeclared as different kind of symbol 2008-04-25 22:53:23 +00:00
mopac
mrbayes - Update maintainer's email address 2008-05-17 16:52:34 +00:00
mummer MUMmer is a modular system for the rapid whole genome alignment of finished 2007-12-14 20:54:47 +00:00
muscle - Update maintainer's email address 2008-05-17 16:52:34 +00:00
nab - Update maintainer's email 2008-04-06 08:39:20 +00:00
ncbi-toolkit - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
njplot - Update maintainer's email address 2008-05-17 16:52:34 +00:00
ortep3 - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
p5-AcePerl - Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN. 2008-04-17 14:30:31 +00:00
p5-Bio-ASN1-EntrezGene - Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN. 2008-04-17 14:30:31 +00:00
p5-Bio-Das Update to 1.08 2008-05-23 12:22:21 +00:00
p5-Bio-Phylo Reset aaron's port maintainerships due to many maintainer-timeouts. 2008-04-29 05:27:09 +00:00
p5-bioperl - Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN. 2008-04-17 14:30:31 +00:00
p5-bioperl-devel Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+. 2007-09-08 01:12:10 +00:00
p5-bioperl-run - Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN. 2008-04-17 14:30:31 +00:00
p5-bioperl-run-devel Welcome bsd.perl.mk. Add support for constructs such as USE_PERL5=5.8.0+. 2007-09-08 01:12:10 +00:00
paml Reset dbader@eece.unm.edu due to maintainer-timeouts. 2007-03-11 03:21:18 +00:00
phd2fasta New port: biology/consed viewing and editing workbench for sequence 2008-05-24 07:03:23 +00:00
phrap New port: biology/consed viewing and editing workbench for sequence 2008-05-24 07:04:45 +00:00
phred New port: biology/consed viewing and editing workbench for sequence 2008-05-24 07:04:45 +00:00
phylip - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
platon - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
povchem - Welcome X.org 7.2 \o/. 2007-05-19 20:36:56 +00:00
primer3 - Update to 1.1.3 2008-04-04 20:46:35 +00:00
protomol - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
psi88 Now we use USE_FORTRAN=yes to use FORTRAN compiler. 2007-07-12 06:41:22 +00:00
py-biopython - Fix typos. 2007-05-31 03:49:14 +00:00
pymol - Add missing dependens 2008-03-27 11:20:17 +00:00
rasmol - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
recombine
ruby-bio - Update to 1.1.0 2007-10-24 01:38:51 +00:00
seaview - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
seqio
sim4
t_coffee - Update to 5.68 2008-04-05 10:47:11 +00:00
tinker - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
treepuzzle
treeviewx - Welcome X.org 7.2 \o/. 2007-05-19 20:36:56 +00:00
tRNAscan-SE - Update MASTER_SITES and WWW: line 2008-05-22 00:49:42 +00:00
wise
xdrawchem - Remove unneeded dependency from gtk12/gtk20 [1] 2008-04-19 17:56:05 +00:00
xmolwt - Welcome X.org 7.2 \o/. 2007-05-19 20:36:56 +00:00
Makefile New port: biology/consed viewing and editing workbench for sequence 2008-05-24 07:04:45 +00:00