Dmitry Marakasov 8dbd1070da Velvet is a de novo genomic assembler specially designed for short read ... sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) WWW: http://www.ebi.ac.uk/~zerbino/velvet/ PR: 140147 Submitted by: Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>		2009-11-07 01:23:59 +00:00
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adun	- fix PORTSCOUT	2009-07-06 07:29:12 +00:00
ariadne
artemis
avida	- Switch SourceForge ports to the new File Release System: categories starting with B,C	2009-08-22 00:15:15 +00:00
babel
belvu
biococoa
biojava
blast
blat
boinc-simap	- Annotate that 8.x no longer needs libmap hack	2009-10-01 07:34:28 +00:00
chemeq
clustalw
consed
crimap
crux	Update to Crux 1.2.0.	2009-09-19 17:58:13 +00:00
distribfold
dna-qc
dotter	UNBREAK: Probably was a temporary failure, checksums are ok now.	2009-09-16 15:57:18 +00:00
embassy	- Update MASTER_SITES	2009-08-14 08:33:22 +00:00
emboss	- Update MASTER_SITES	2009-08-14 08:33:22 +00:00
fasta
fasta3	Update to 35.4.9	2009-08-23 15:47:37 +00:00
fastdnaml
finchtv
fluctuate
garlic
genpak	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
gff2ps
gmap
gperiodic	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
grappa
hmmer
iolib	Io_lib is a library of file reading and writing code to provide a	2009-08-28 23:34:20 +00:00
jalview
kinemage
L-Breeder	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
lagan
lamarc
libgenome	-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.	2009-08-02 19:36:34 +00:00
libsbml	- Update to 4.0.0	2009-09-23 01:06:29 +00:00
linux-foldingathome
lsysexp	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
mafft
mapm3
migrate
molden	Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now	2009-09-13 00:08:01 +00:00
mopac	- Switch SourceForge ports to the new File Release System: categories starting with B,C	2009-08-22 00:15:15 +00:00
mrbayes
mummer	- Update to 3.21.	2009-08-28 14:52:05 +00:00
muscle
ncbi-toolkit
njplot	Convert most of remaining ports that depend on xorg-libraries to	2009-06-09 15:33:28 +00:00
ortep3	Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now	2009-09-13 00:08:01 +00:00
p5-AcePerl	- Flip MAKE_JOBS_SAFE to MAKE_JOBS_UNSAFE	2009-07-07 22:11:07 +00:00
p5-Bio-ASN1-EntrezGene
p5-Bio-Das	- Update to 1.14	2009-09-08 12:08:12 +00:00
p5-Bio-Glite
p5-Bio-Graphics	- Update to 0.982	2009-08-28 23:36:45 +00:00
p5-Bio-MAGETAB	Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plists	2009-07-30 23:04:49 +00:00
p5-Bio-NEXUS	Bio::NEXUS package provides an object-oriented, Perl-based	2009-08-22 20:39:51 +00:00
p5-Bio-Phylo	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
p5-Bio-SCF	Bio::SCF module allows you to read and update (in a restricted	2009-08-28 23:36:09 +00:00
p5-bioperl	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
p5-bioperl-run	- Relax check on bioperl version; people keep forgetting to update this check	2009-08-02 20:00:08 +00:00
paml	- Update to 4.3	2009-08-13 17:00:04 +00:00
phd2fasta
phrap
phred
phylip	-Update to 3.69	2009-09-16 14:27:00 +00:00
phyml	PhyML is a software that estimates maximum likelihood phylogenies from	2009-07-21 01:10:13 +00:00
platon	Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now	2009-09-13 00:08:01 +00:00
povchem
primer3
protomol	- Switch SourceForge ports to the new File Release System: categories starting with B,C	2009-08-22 00:15:15 +00:00
psi88	Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now	2009-09-13 00:08:01 +00:00
py-biopython	- Update to 138038	2009-09-04 20:41:25 +00:00
pycogent	- Switch SourceForge ports to the new File Release System: categories starting with B,C	2009-08-22 00:15:15 +00:00
pymol	- Update lang/python26 and make Python 2.6.2 to the default Python version	2009-06-08 22:30:55 +00:00
rasmol	Convert most of remaining ports that depend on xorg-libraries to	2009-06-09 15:33:28 +00:00
recombine
ruby-bio
seaview	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
seqio
sim4
ssaha
t_coffee
tinker	Bump PORTREVISION for everything that sets USE_FORTRAN=yes which now	2009-09-13 00:08:01 +00:00
treepuzzle
treeviewx	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
tRNAscan-SE
velvet	Velvet is a de novo genomic assembler specially designed for short read	2009-11-07 01:23:59 +00:00
wise
xdrawchem	- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated	2009-07-31 13:57:52 +00:00
xmolwt
Makefile	Velvet is a de novo genomic assembler specially designed for short read	2009-11-07 01:23:59 +00:00