| .. |
|
abyss
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
|
|
|
bcftools
|
|
|
|
bedtools
|
biology/bedtools: unbreak with libc++ 8
|
2019-03-04 06:55:08 +00:00 |
|
biococoa
|
Move Objective-C ports to the v2 GNUstep ABI.
|
2019-02-03 15:37:58 +00:00 |
|
bowtie
|
|
|
|
bowtie2
|
biology/bowtie2: Clarify CPU-specificity
|
2019-04-24 17:41:27 +00:00 |
|
bwa
|
|
|
|
canu
|
biology/canu: Fix build on powerpc64 and aarch64
|
2019-04-18 12:15:56 +00:00 |
|
cd-hit
|
biology/cd-hit: Upgrade to 4.8.1
|
2019-03-14 23:59:47 +00:00 |
|
cdbfasta
|
|
|
|
checkm
|
Bump a few PORTREVISIONs after r498529
|
2019-04-10 06:18:31 +00:00 |
|
chemeq
|
|
|
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
consed
|
|
|
|
cytoscape
|
|
|
|
ddocent
|
|
|
|
diamond
|
|
|
|
dsr-pdb
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
emboss
|
|
|
|
exonerate
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastahack
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastqc
|
|
|
|
fasttree
|
|
|
|
fastx-toolkit
|
|
|
|
figtree
|
New port: biology/figtree: Graphical viewer of phylogenetic trees
|
2019-02-03 21:14:38 +00:00 |
|
fluctuate
|
|
|
|
freebayes
|
|
|
|
garlic
|
|
|
|
gatk
|
|
|
|
gff2ps
|
|
|
|
gmap
|
|
|
|
gperiodic
|
|
|
|
graphlan
|
New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees
|
2019-02-03 20:13:26 +00:00 |
|
grappa
|
|
|
|
groopm
|
|
|
|
hisat2
|
|
|
|
hmmer
|
vec_splats function is not supported by base GCC. Add USES=compiler:c11
|
2019-02-18 01:30:24 +00:00 |
|
htslib
|
|
|
|
hyphy
|
|
|
|
igv
|
biology/igv: Update 2.4.19 -> 2.5.0
|
2019-04-04 04:49:41 +00:00 |
|
infernal
|
|
|
|
iolib
|
- Fix build in head i386
|
2019-04-01 19:33:15 +00:00 |
|
iqtree
|
biology/iqtree: Update to version 1.6.10
|
2019-02-21 14:33:43 +00:00 |
|
jalview
|
|
|
|
jellyfish
|
|
|
|
kallisto
|
kallisto: Upgrade to 0.45.1, unbundle hstlib
|
2019-02-24 20:32:19 +00:00 |
|
lagan
|
|
|
|
lamarc
|
|
|
|
libgtextutils
|
|
|
|
libsbml
|
|
|
|
linux-foldingathome
|
|
|
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
minimap2
|
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences
|
2019-04-24 18:03:49 +00:00 |
|
molden
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
mopac
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
mrbayes
|
Update devel/readline to 8.0
|
2019-04-09 14:04:49 +00:00 |
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
Update dns/libidn2 to 2.1.1
|
2019-02-09 23:25:36 +00:00 |
|
ncbi-cxx-toolkit
|
|
|
|
ncbi-toolkit
|
Update dns/libidn2 to 2.1.1
|
2019-02-09 23:25:36 +00:00 |
|
ngs-sdk
|
biology/ngs-sdk: Update 2.9.4 -> 2.9.6
|
2019-03-31 03:31:59 +00:00 |
|
p5-AcePerl
|
|
|
|
p5-Bio-ASN1-EntrezGene
|
|
|
|
p5-Bio-Cluster
|
Add p5-Bio-Cluster 1.7.3
|
2019-02-20 20:46:37 +00:00 |
|
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
|
Fix typo
|
2019-04-23 14:11:50 +00:00 |
|
p5-Bio-NEXUS
|
|
|
|
p5-Bio-Phylo
|
|
|
|
p5-Bio-SCF
|
- Add LICENSE
|
2019-03-30 09:01:08 +00:00 |
|
p5-BioPerl
|
Update to 1.007005 (1.7.5)
|
2019-02-22 19:54:12 +00:00 |
|
p5-BioPerl-Run
|
Update to 1.007003
|
2019-02-20 20:46:58 +00:00 |
|
p5-transdecoder
|
|
|
|
p5-TrimGalore
|
biology/p5-TrimGalore: Upgrade to 0.6.1
|
2019-03-24 21:44:17 +00:00 |
|
paml
|
biology/paml: Update to version 4.9i
|
2019-02-26 15:12:42 +00:00 |
|
pbbam
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
pbcopper
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
pbseqan
|
biology/pbseqan: Mark deprecated
|
2019-02-20 01:53:35 +00:00 |
|
pear-merger
|
|
|
|
phrap
|
|
|
|
phred
|
|
|
|
phylip
|
|
|
|
phyml
|
|
|
|
plinkseq
|
|
|
|
primer3
|
|
|
|
prodigal
|
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes
|
2019-02-03 18:08:14 +00:00 |
|
prodigy-lig
|
New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities
|
2019-02-03 18:49:23 +00:00 |
|
protomol
|
|
|
|
psi88
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
py-biom-format
|
Bump a few PORTREVISIONs after r498529
|
2019-04-10 06:18:31 +00:00 |
|
py-biopython
|
|
|
|
py-bx-python
|
|
|
|
py-cutadapt
|
Bump a few PORTREVISIONs after r498529
|
2019-04-10 06:18:31 +00:00 |
|
py-dnaio
|
biology/py-dnaio: Read and write FASTQ and FASTA
|
2019-03-24 19:40:26 +00:00 |
|
py-fastTSNE
|
biology/py-fastTSNE: Add the PORTSCOUT line
|
2019-03-31 16:57:54 +00:00 |
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
Bump a few PORTREVISIONs after r498529
|
2019-04-10 06:18:31 +00:00 |
|
py-gtfparse
|
|
|
|
py-loompy
|
biology/py-loompy: Update 2.0.16 -> 2.0.17
|
2019-02-02 21:38:48 +00:00 |
|
py-macs2
|
|
|
|
py-orange3-bioinformatics
|
|
|
|
py-orange3-single-cell
|
|
|
|
py-pyfaidx
|
Bump a few PORTREVISIONs after r498529
|
2019-04-10 06:18:31 +00:00 |
|
py-pysam
|
|
|
|
py-xenaPython
|
New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub
|
2019-04-12 17:01:10 +00:00 |
|
pycogent
|
|
|
|
pyfasta
|
- Update WWW
|
2019-02-07 09:30:40 +00:00 |
|
python-nexus
|
|
|
|
rainbow
|
|
|
|
recombine
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
samtools
|
|
|
|
seaview
|
|
|
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
seqio
|
|
|
|
seqtk
|
|
|
|
seqtools
|
|
|
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
stacks
|
|
|
|
star
|
biology/star: Modify PKGBASE to avoid conflict with archivers/star
|
2019-04-23 15:03:29 +00:00 |
|
stringtie
|
|
|
|
t_coffee
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
tabixpp
|
|
|
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ugene
|
|
|
|
unanimity
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
vcflib
|
|
|
|
vcftools
|
|
|
|
velvet
|
|
|
|
wise
|
|
|
|
Makefile
|
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences
|
2019-04-24 18:03:49 +00:00 |
196e812dbd