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Rene Ladan 06a0710b7a biology/py-orange3-bioinformatics: Remove expired port 4 days ago
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R-cran-Biobase biology/R-cran-Biobase: Update to 2.66.0 3 months ago
R-cran-BiocGenerics biology/R-cran-BiocGenerics: Update to 0.52.0 3 months ago
R-cran-BiocManager biology/R-cran-BiocManager: Return to pool 2 months ago
abyss Mk/bsd.commands.mk: Use absolute path to define GMAKE 6 months ago
ad2vcf biology/ad2vcf: Update to 0.1.6.19 1 year ago
andi biology/andi: New ports: Efficient estimation of evolutionary distances 10 months ago
artemis Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
atac-seq all: remove support for expired FreeBSD 13.3 6 months ago
augustus devel/boost: bump consumers after Boost update 4 weeks ago
avida */*: Sunset 12.4-RELEASE/12-STABLE from ports tree 2 years ago
babel biology/babel: Update WWW 2 years ago
bamtools biology/bamtools: Update to 2.5.3 1 month ago
bamutil Remove WWW entries moved into port Makefiles 3 years ago
barrnap biology/barrnap: Update descr 3 years ago
bbmap biology/bbmap: Update to 39.15 5 months ago
bcf-score biology/bcf-score: Use latest versions of hstlib and bcftools 6 days ago
bcftools biology/bcftools: Update to 1.22 3 weeks ago
bedtools biology/bedtools: Update to 2.31.1 2 years ago
bfc Remove WWW entries moved into port Makefiles 3 years ago
bifrost biology/bifrost: Remove USE_GCC, fix build with clang19 1 month ago
bio-mocha biology/bio-mocha: Use latest versions of htslib and bcftools 6 days ago
bioawk Remove WWW entries moved into port Makefiles 3 years ago
biococoa */*: Convert to USES=tar:tgz 4 weeks ago
biolibc biology/biolibc: Update to 0.2.7 2 months ago
biolibc-tools biology/biolibc-tools: Update to 0.1.5 2 months ago
bioparser biology/bioparser: update 3.0.15 → 3.1.0 2 years ago
biosig */*: bump PORTREVISION after the upgrade to Suitesparse 6 months ago
biosoup biology/biosoup: Install cmake files 2 years ago
biostar-tools biology/biostar-tools: Update to 2.0 8 months ago
bolt-lmm devel/boost: bump consumers after Boost update 4 weeks ago
bowtie */*: Update WWW to use HTTPS for sourceforge.net projects 2 years ago
bowtie2 biology/bowtie2: Update to 2.5.4 1 year ago
btllib biology/btllib: update 1.7.3 → 1.7.5 7 months ago
bwa biology/bwa: update 0.7.18 => 0.7.19 3 months ago
canu devel/boost: bump consumers after Boost update 4 weeks ago
cd-hit biology/cd-hit: allow to build without GCC on libomp-less systems 2 years ago
cdbfasta biology/cdbfasta: Update to 2023.07.10 2 years ago
chip-seq biology/chip-seq: Metaport for ChIP-Seq analysis 2 years ago
clustal-omega Remove WWW entries moved into port Makefiles 3 years ago
clustalw biology/clustalw: Unbreak build for clang 16 2 years ago
coverm lang/rust: Bump revisions after 1.87.0 3 weeks ago
cufflinks devel/boost: bump consumers after Boost update 4 weeks ago
cytoscape Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
ddocent Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
diamond biology/diamond: Update to 2.1.11 5 months ago
dsr-pdb devel/boost: bump consumers after Boost update 4 weeks ago
edlib Remove WWW entries moved into port Makefiles 3 years ago
emboss */*: Refactor with IGNORE_WITH_MYSQL 2 years ago
erminej Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
exonerate biology/exonerate: remove maintainer (email address gone) 8 months ago
fasda biology/fasda: Update to 0.2.0.1 1 month ago
fasda-utils biology/fasda-utils: Update to 0.1.0.2 2 months ago
fasta MAN[1-5]PREFIX: eleminate its usage and move man to share/man 1 year ago
fasta3 MAN?PREFIX: eleminate its usage and move man to share/man 1 year ago
fastahack Remove WWW entries moved into port Makefiles 3 years ago
fastani biology/fastani: Broken where OpenMP isn't available; Update WWW 8 months ago
fastdnaml Remove WWW entries moved into port Makefiles 3 years ago
fastool Remove WWW entries moved into port Makefiles 3 years ago
fastp biology/fastp: Update to 0.26.0 3 weeks ago
fastq-trim biology/fastq-trim: Update to 0.1.4 2 months ago
fastqc Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
fasttree biology/fasttree: Update to 2.1.11 7 months ago
fastx-toolkit biology/fastx-toolkit: Unbreak build on 14-CURRENT 2 years ago
fermi-lite biology/fermi-lite: enable on powerpc64le 5 months ago
figtree Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
flash Remove WWW entries moved into port Makefiles 3 years ago
fluctuate Remove WWW entries moved into port Makefiles 3 years ago
freebayes biology/freebayes: Update to 1.3.9 4 months ago
garlic Remove WWW entries moved into port Makefiles 3 years ago
gatk biology/gatk: Update WWW 4 months ago
gcta */*: bump PORTREVISION after OpenBLAS upgrade 5 months ago
gemma */*: bump PORTREVISION after OpenBLAS upgrade 5 months ago
generand biology/generand: Move man pages to share/man 1 year ago
gff2ps biology/gff2ps: drop maintainership 2 years ago
gffread Remove WWW entries moved into port Makefiles 3 years ago
gkl Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
gmap Remove WWW entries moved into port Makefiles 3 years ago
gperiodic gnome.mk: rename gdkpixbuf2 to gdkpixbuf to prepare for port move 3 months ago
graphlan Remove WWW entries moved into port Makefiles 3 years ago
groopm python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
haplohseq devel/boost: bump consumers after Boost update 4 weeks ago
hhsuite */*: bump PORTREVISION after OpenMPI upgrade 1 year ago
hisat2 Remove WWW entries moved into port Makefiles 3 years ago
hmmer biology/hmmer: update to 3.4 8 months ago
htslib biology/htslib: Update to 1.22 3 weeks ago
hyphy biology/hyphy: Update to 2.5.73 1 month ago
igv Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
infernal biology/infernal: update 1.1.4 → 1.1.5 5 months ago
iolib biology/iolib: Moved man to share/man 1 year ago
iqtree devel/boost: bump consumers after Boost update 4 weeks ago
jalview Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
jellyfish biology/jellyfish: Move man pages to share/man 1 year ago
kallisto biology/kallisto: Remove USE_GCC, fix build with clang19 1 month ago
kmcp various: Bump PORTREVISION after go124-1.24.4 update 3 weeks ago
lamarc biology/lamarc: New maintainer hayzam@alchemilla.io 1 month ago
libbigwig biology/libbigwig: update 0.4.7 → 0.4.8 5 months ago
libcombine biology/libcombine: Fix build with libsbml 5.20.0 2 years ago
libgff Remove WWW entries moved into port Makefiles 3 years ago
libgtextutils Remove WWW entries moved into port Makefiles 3 years ago
libneurosim devel/automake: Update to 1.17 11 months ago
libnuml biology/{,py-}libnuml: update 1.1.6 → 1.1.7 3 months ago
libsbml biology/libsbml: Update to 5.20.5 1 month ago
libsedml biology/{,py-}libsedml: update 2.0.32 → 2.0.33 2 months ago
linux-foldingathome biology/linux-foldingathome: Use USES=tar 4 weeks ago
locarna biology/locarna: Move man pages to share/man 1 year ago
mafft biology/mafft: Moved man to share/man 1 year ago
mapm3 Remove WWW entries moved into port Makefiles 3 years ago
mashmap biology/mashmap: Broken on armv7 1 year ago
mca-calling biology/mca-calling: Core tools for mCA event calling 8 months ago
megahit biology/megahit: Update to 1.2.9.20 1 month ago
metaeuk biology/metaeuk: builds now fine on powerpc64le 5 months ago
migrate biology/migrate: fix build on !x86 12 months ago
minimap2 biology/minimap2: Remove extraneous file that snuck in the last commit 6 days ago
mmseqs2 biology/mmseqs2: Update to 17.b804.f 5 months ago
molden all: return jmd's ports to the pool after safekeeping their commit bit. 7 months ago
mothur biology/mothur: update 1.48.1 → 1.48.2 8 months ago
mrbayes Remove WWW entries moved into port Makefiles 3 years ago
mummer biology/mummer: update 4.0.0 → 4.0.1 5 months ago
muscle Remove WWW entries moved into port Makefiles 3 years ago
ncbi-blast+ devel/grpc: Update to 1.73.0 1 week ago
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Broken on i386 4 months ago
ncbi-entrez-direct various: Bump PORTREVISION after go124-1.24.4 update 3 weeks ago
ncbi-toolkit all: drop support for expired FreeBSD 14.0 9 months ago
ngs-sdk biology/ngs-sdk: Attempt to fix build on i386 1 year ago
p5-AcePerl Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-ASN1-EntrezGene Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Cluster Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Coordinate Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-DB-EMBL Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-DB-NCBIHelper biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8 2 years ago
p5-Bio-Das Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Das-Lite Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-FeatureIO Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-GFF3 Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Glite Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Graphics Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-MAGETAB Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-NEXUS Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Phylo Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-SCF Remove WWW entries moved into port Makefiles 3 years ago
p5-Bio-Variation Remove WWW entries moved into port Makefiles 3 years ago
p5-BioPerl biology/p5-BioPerl: Update to 1.007008 2 years ago
p5-BioPerl-Run Remove WWW entries moved into port Makefiles 3 years ago
p5-TrimGalore perl@: adopt a few ports 1 month ago
p5-transdecoder p5-transdecoder: Update to 5.7.1 2 years ago
paml biology/paml: Update to 4.10.9 1 month ago
pbbam devel/boost: bump consumers after Boost update 4 weeks ago
peak-classifier biology/peak-classifier: Clean up USES=python 1 year ago
pear-merger MANPREFIX: eliminate its usage 1 year ago
phrap Remove WWW entries moved into port Makefiles 3 years ago
phred Remove WWW entries moved into port Makefiles 3 years ago
phyml biology/phyml: fix build on non-amd64 1 year ago
picard-tools Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
plink */*: bump PORTREVISION after OpenBLAS upgrade 5 months ago
pooler biology/pooler: Update to 1.89 5 months ago
preseq preseq: Not for 32-bit platforms 7 months ago
primer3 biology/primer3: Fix build with llvm16 2 years ago
prodigal biology/prodigal: Update 2.6.3-7 → 2.6.3-16 2 years ago
prodigy-lig biology/prodigy-lig: update 1.1.2 → 1.1.3 9 months ago
protomol graphics/tiff: Update to 4.6.0 1 year ago
psi88 *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2 years ago
py-Genesis-PyAPI python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-PySCeS biology/py-PySCeS: update 1.2.1 → 1.2.2 11 months ago
py-bcbio-gff python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-biom-format python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-biopython python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-biosig python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 1 week ago
py-bx-python Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test} 3 months ago
py-crossmap python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-cutadapt biology/py-cutadapt: update to 5.1 3 weeks ago
py-deeptools python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-deeptoolsintervals python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-dna-features-viewer python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-dnaio Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test} 3 months ago
py-ete3 python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-gffutils python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-goatools python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-gtfparse biology/py-gtfparse: Fix fetch 7 months ago
py-hits python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-htseq python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-libnuml biology/{,py-}libnuml: update 1.1.6 → 1.1.7 3 months ago
py-libsedml biology/{,py-}libsedml: update 2.0.32 → 2.0.33 2 months ago
py-loompy python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-macs2 python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-macs3 Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test} 3 months ago
py-mrcfile python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-multiqc python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-newick biology/py-newick: Update to 1.10.0 3 months ago
py-ont-fast5-api python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-pandas-charm python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-py2bit python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-pybigwig python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-pydeseq2 biology/py-pydeseq2: Python reimplementation of the DESeq2 R package 2 weeks ago
py-pyfaidx python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-pyrodigal python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 1 week ago
py-pysam python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 1 week ago
py-python-libsbml python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 1 week ago
py-pywgsim python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-resdk biology/py-resdk: update 21.2.1 → 22.0.0 3 months ago
py-scikit-bio python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 1 week ago
py-valerius python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
py-xenaPython python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
pyfasta python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
python-nexus python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 4 months ago
rainbow Remove WWW entries moved into port Makefiles 3 years ago
rampler *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2 years ago
readseq Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
rna-seq biology/rna-seq: Add biology/star dep to metaport 2 years ago
ruby-bio Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2 years ago
rubygem-bio biology/rubygem-bio: Update to 2.0.6 3 months ago
rubygem-bio-executables Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2 years ago
rubygem-bio-old-biofetch-emulator Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2 years ago
rubygem-bio-shell Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2 years ago
salmon devel/boost: bump consumers after Boost update 4 weeks ago
sam2pairwise Remove WWW entries moved into port Makefiles 3 years ago
samtools biology/samtools: Update to 1.22 3 weeks ago
scrm biology/scrm: Move man pages to share/man 1 year ago
seaview biology/seaview: Update version 5.0.5=>5.1 3 months ago
seqan Remove WWW entries moved into port Makefiles 3 years ago
seqan-apps biology/seqan-apps: Fix build with llvm16 2 years ago
seqan1 Remove WWW entries moved into port Makefiles 3 years ago
seqan3 biology/seqan3: update 3.2.0 → 3.3.0 2 years ago
seqkit various: Bump PORTREVISION after go124-1.24.4 update 3 weeks ago
seqtk biology/seqtk: Update to 1.5 3 weeks ago
seqwish biology/seqwish: Set OPENMP=OFF and broken where OpenMP isn't available 4 months ago
sigviewer *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2 years ago
slclust Remove WWW entries moved into port Makefiles 3 years ago
smithwaterman Remove WWW entries moved into port Makefiles 3 years ago
snpeff Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
spoa biology/spoa: Broken on i386 1 year ago
sra-tools biology/sra-tools: Update to 3.2.1 3 months ago
stacks biology/stacks: fix build without libomp 5 months ago
star biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir 1 year ago
stringtie Remove WWW entries moved into port Makefiles 3 years ago
subread biology/subread: Update to 2.1.0 3 months ago
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.11 3 years ago
tabixpp biology/tabixpp: Undeprecate and update to 1.1.2 4 months ago
taxonkit various: Bump PORTREVISION after go124-1.24.4 update 3 weeks ago
treekin */*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS 5 months ago
treepuzzle Remove WWW entries moved into port Makefiles 3 years ago
trimadap biology/trimadap: drop not necessary powerpc64le knob 5 months ago
trimmomatic Mk/**java.mk: Convert bsd.java.mk to USES 6 months ago
ucsc-userapps biology/ucsc-userapps: Update to v474 7 months ago
ugene MAN?PREFIX: eleminate its usage and move man to share/man 1 year ago
unikmer various: Bump PORTREVISION after go124-1.24.4 update 3 weeks ago
vcf-split biology/vcf-split: Move man pages to share/man 1 year ago
vcf2hap biology/vcf2hap: Move man pages to share/man 1 year ago
vcflib python.mk: rename PYTHON_EXT_SUFFIX to PYTHON_TAG, document, etc 1 week ago
vcftools biology/vcftools: Update to 0.1.17 1 month ago
velvet Remove WWW entries moved into port Makefiles 3 years ago
viennarna */*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS 5 months ago
vsearch biology/vsearch: Update to 2.30.0 4 months ago
vt biology/vt: Bump PORTREVISION for biology/htslib update 3 years ago
wfa2-lib biology/wfa2-lib: fix build without libomp 11 months ago
wise all: drop support for expired FreeBSD 14.0 9 months ago
Makefile biology/py-orange3-bioinformatics: Remove expired port 4 days ago