Wen Heping ec07b546cf DNA query sequences against a protein reference database (BLASTP and BLASTX ... alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca		2016-05-06 08:45:02 +00:00
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ariadne
artemis
avida
babel
bcftools	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
bedtools	The bedtools utilities are a suite of tools for performing a wide range of	2016-01-19 08:56:34 +00:00
biococoa
biojava
blat	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
bowtie	New port: biology/bowtie.	2016-03-05 13:21:26 +00:00
bowtie2	New port: biology/bowtie2.	2016-03-23 11:22:39 +00:00
bwa
cd-hit
cdbfasta
chemeq	- Add LICENSE	2016-04-10 11:24:32 +00:00
clustalw
consed	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
crux	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
diamond	DNA query sequences against a protein reference database (BLASTP and BLASTX	2016-05-06 08:45:02 +00:00
emboss	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
fasta
fasta3
fastdnaml	Convert LICENSE= "GPLxx # or later" to "GPLxx+"	2016-01-12 16:20:31 +00:00
fastool
fasttree
fastx-toolkit	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
fluctuate
garlic
gff2ps	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
gmap
gperiodic
grappa
hmmer
htslib	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
iolib	- Update to 1.14.8	2016-05-01 01:03:48 +00:00
jalview
jellyfish	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
lagan	Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRS	2016-01-09 18:26:40 +00:00
lamarc	Cleanup GH_* and variables order.	2015-12-29 14:30:46 +00:00
libgtextutils	Cleanup GH_* and variables order.	2015-12-29 14:30:46 +00:00
libsbml	Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:	2016-04-16 01:54:15 +00:00
linux-foldingathome
mafft
mapm3	biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGS	2016-02-01 22:09:10 +00:00
migrate	- Switch to options helpers	2016-04-17 10:15:59 +00:00
molden	biology/molden: updated distfile, take maintainer	2016-01-20 19:31:52 +00:00
mopac	Convert LICENSE= "GPLxx # or later" to "GPLxx+"	2016-01-12 16:20:31 +00:00
mrbayes
mummer
muscle
ncbi-blast+	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
ncbi-toolkit
p5-AcePerl	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-ASN1-EntrezGene	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-Das	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-Das-Lite	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-GFF3	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-Glite	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-Graphics	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-MAGETAB	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-NEXUS	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-Phylo	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-Bio-SCF	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-bioperl	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-bioperl-run	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
p5-transdecoder	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
paml
phrap
phred
phylip	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
phyml	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
platon
plink	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
plinkseq	many ports: mark broken on powerpc64	2016-04-21 16:43:14 +00:00
primer3
protomol	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
psi88	- Switch to options helpers	2016-04-16 06:38:23 +00:00
py-biopython	- Update to 1.66	2016-04-17 03:55:01 +00:00
pycogent	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
pyfasta
python-nexus	- Update to 1.34	2016-02-12 13:18:37 +00:00
recombine
ruby-bio	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
samtools	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
seaview	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
seqan
seqio
seqtools	biology/seqtools: 4.41.1 -> 4.42.1	2016-04-22 16:27:25 +00:00
sim4
slclust	New port: biology/slclust.	2016-03-23 11:00:44 +00:00
ssaha
t_coffee	Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.	2016-04-01 13:29:15 +00:00
tinker
treepuzzle
treeviewx	Convert LICENSE= "GPLxx # or later" to "GPLxx+"	2016-01-12 16:20:31 +00:00
trimmomatic	Trimmomatic performs a variety of useful trimming tasks for illumina	2016-03-17 08:21:14 +00:00
tRNAscan-SE
ugene	Update to version 1.22.0, which now unfortunately requires Qt 5.x. Also	2016-04-14 04:07:44 +00:00
vcftools	New port: biology/vcftools.	2016-02-26 17:07:59 +00:00
velvet
wise
xmolwt
Makefile	DNA query sequences against a protein reference database (BLASTP and BLASTX	2016-05-06 08:45:02 +00:00