| .. |
|
ariadne
|
Deprecate ports broken for more than 6 months
|
2018-05-05 10:49:36 +00:00 |
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
|
|
|
bcftools
|
|
|
|
bedtools
|
biology/bedtools: Upgrade to 2.27.1
|
2018-04-19 16:44:59 +00:00 |
|
biococoa
|
|
|
|
blat
|
|
|
|
bowtie
|
|
|
|
bowtie2
|
|
|
|
bwa
|
|
|
|
canu
|
biology/canu: Upgrade to 1.7 release
|
2018-04-26 04:16:15 +00:00 |
|
cd-hit
|
|
|
|
cdbfasta
|
|
|
|
chemeq
|
|
|
|
clustalw
|
|
|
|
consed
|
|
|
|
crux
|
Deprecate ports broken for more than 6 months
|
2018-05-05 10:49:36 +00:00 |
|
ddocent
|
biology/ddocent: Bash pipeline for RAD sequencing
|
2018-04-20 01:34:05 +00:00 |
|
diamond
|
biology/diamond: Update to version 0.9.21
|
2018-04-20 21:23:27 +00:00 |
|
emboss
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastahack
|
biology/fastahack: Utility for indexing and sequence extraction from FASTA files
|
2018-04-16 14:50:46 +00:00 |
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastqc
|
|
|
|
fasttree
|
|
|
|
fastx-toolkit
|
|
|
|
fluctuate
|
|
|
|
freebayes
|
biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping
|
2018-04-20 00:07:27 +00:00 |
|
garlic
|
|
|
|
gff2ps
|
|
|
|
gmap
|
|
|
|
gperiodic
|
|
|
|
grappa
|
|
|
|
hmmer
|
|
|
|
htslib
|
|
|
|
hyphy
|
New port, biology/hyphy: Hypothesis testing using Phylogenies
|
2018-05-11 00:05:16 +00:00 |
|
iolib
|
|
|
|
iqtree
|
biology/iqtree: Update to version 1.6.5
|
2018-05-11 16:57:09 +00:00 |
|
jalview
|
|
|
|
jellyfish
|
|
|
|
kallisto
|
|
|
|
lagan
|
|
|
|
lamarc
|
|
|
|
libgtextutils
|
|
|
|
libsbml
|
|
|
|
linux-foldingathome
|
|
|
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
molden
|
Mark BROKEN: checksum and size mismatch
|
2018-05-07 05:34:10 +00:00 |
|
mopac
|
|
|
|
mrbayes
|
|
|
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
|
|
|
ncbi-toolkit
|
|
|
|
njplot
|
|
|
|
p5-AcePerl
|
|
|
|
p5-Bio-ASN1-EntrezGene
|
|
|
|
p5-Bio-Coordinate
|
|
|
|
p5-Bio-Das
|
|
|
|
p5-Bio-Das-Lite
|
|
|
|
p5-Bio-FeatureIO
|
|
|
|
p5-Bio-GFF3
|
|
|
|
p5-Bio-Glite
|
|
|
|
p5-Bio-Graphics
|
|
|
|
p5-Bio-MAGETAB
|
|
|
|
p5-Bio-NEXUS
|
|
|
|
p5-Bio-Phylo
|
|
|
|
p5-Bio-SCF
|
|
|
|
p5-BioPerl
|
|
|
|
p5-BioPerl-Run
|
|
|
|
p5-transdecoder
|
|
|
|
p5-TrimGalore
|
|
|
|
paml
|
biology/paml: Set PORTVERSION directly
|
2018-04-26 15:36:30 +00:00 |
|
pbbam
|
biology/pbbam: PacBio BAM C++ library, with SWIG bindings
|
2018-04-23 16:08:21 +00:00 |
|
pbcopper
|
biology/pbcopper: Core C++ library for Pacific Biosciences tools
|
2018-04-23 16:23:53 +00:00 |
|
pbseqan
|
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn
|
2018-04-21 17:21:30 +00:00 |
|
pear-merger
|
biology/pear-merger: Memory-efficient and accurate paired-end read merger
|
2018-04-04 17:21:39 +00:00 |
|
phrap
|
|
|
|
phred
|
|
|
|
phylip
|
|
|
|
phyml
|
|
|
|
plink
|
Deprecate ports broken for more than 6 months
|
2018-05-05 10:49:36 +00:00 |
|
plinkseq
|
|
|
|
primer3
|
|
|
|
protomol
|
|
|
|
psi88
|
|
|
|
py-biom-format
|
|
|
|
py-biopython
|
- Update to 1.71
|
2018-04-09 06:26:18 +00:00 |
|
py-bx-python
|
|
|
|
py-cutadapt
|
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
|
2018-04-25 16:42:37 +00:00 |
|
py-macs2
|
|
|
|
py-pysam
|
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
|
2018-04-25 16:42:37 +00:00 |
|
pycogent
|
|
|
|
pyfasta
|
|
|
|
python-nexus
|
|
|
|
rainbow
|
|
|
|
recombine
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
samtools
|
|
|
|
seaview
|
biology/seaview: Update version 4.6.3=>4.6.5
|
2018-04-24 12:31:32 +00:00 |
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
devel/boost-*: update to 1.67.0
|
2018-04-18 13:57:42 +00:00 |
|
seqio
|
|
|
|
seqtk
|
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
|
2018-04-03 20:57:05 +00:00 |
|
seqtools
|
|
|
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
|
2018-04-15 17:45:52 +00:00 |
|
ssaha
|
Deprecate ports broken for more than 6 months
|
2018-05-05 10:49:36 +00:00 |
|
stacks
|
|
|
|
t_coffee
|
|
|
|
tabixpp
|
biology/tabixpp: C++ wrapper to tabix indexer
|
2018-04-14 23:52:16 +00:00 |
|
tinker
|
|
|
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
Deprecate ports broken for more than 6 months
|
2018-05-05 10:49:36 +00:00 |
|
ugene
|
|
|
|
unanimity
|
biology/unanimity: Pacific Biosciences consensus library and applications
|
2018-04-24 14:16:46 +00:00 |
|
vcflib
|
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files
|
2018-04-17 03:11:39 +00:00 |
|
vcftools
|
|
|
|
velvet
|
|
|
|
wise
|
|
|
|
xmolwt
|
|
|
|
Makefile
|
New port, biology/hyphy: Hypothesis testing using Phylogenies
|
2018-05-11 00:05:16 +00:00 |
