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freebsd-ports/biology
History
Christian Weisgerber feb1fa34f5 audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
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abyss
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
ad2vcf
…
artemis
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atac-seq
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
augustus
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
avida
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babel
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bamtools
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bamutil
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barrnap
…
bbmap
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bcf-score
biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics
2023-02-25 08:27:46 -06:00
bcftools
biology/bcftools: Update to 1.17
2023-02-24 17:30:58 -06:00
bedtools
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bfc
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bio-mocha
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bioawk
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biococoa
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
biolibc
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biolibc-tools
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bioparser
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biosig
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
biosoup
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
biostar-tools
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
bolt-lmm
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
bowtie
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bowtie2
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bwa
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canu
*/*: Refactor java/openjdk7 removal
2023-04-04 13:10:53 -05:00
cd-hit
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cdbfasta
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checkm
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
clustal-omega
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clustalw
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cufflinks
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
cytoscape
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ddocent
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
diamond
biology/diamond: Update to 2.1.6
2023-03-18 12:49:03 -03:00
dsr-pdb
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edlib
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emboss
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erminej
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exonerate
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fasda
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fasta
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fasta3
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fastahack
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fastdnaml
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fastool
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fastp
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
fastq-trim
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fastqc
biology/fastqc: Update to 0.12.1
2023-03-04 18:17:20 -06:00
fasttree
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fastx-toolkit
biology/fastx-toolkit: Unbreak build on 14-CURRENT
2023-03-07 11:28:13 -06:00
figtree
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flash
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fluctuate
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freebayes
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garlic
…
gatk
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gcta
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
gemma
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
generand
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gff2ps
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gffread
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gmap
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gperiodic
accessibility/at-spi2-core: update to 2.46.0
2023-03-02 06:23:10 +01:00
graphlan
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groopm
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
haplohseq
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
hhsuite
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
hisat2
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hmmer
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htslib
biology/htslib: fix build on armv7
2023-04-18 23:55:29 +02:00
hyphy
biology/hyphy: Update to 2.5.50
2023-04-19 13:30:57 -03:00
igv
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
infernal
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iolib
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iqtree
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
jalview
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jellyfish
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kallisto
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
kmcp
all: Bump PORTREVISION after lang/go{119,120} update
2023-04-08 10:13:25 -05:00
lamarc
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libbigwig
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libcombine
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libgff
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libgtextutils
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libneurosim
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libnuml
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libsbml
biology/libsbml: Update WWW and clean up pkg-descr
2023-04-06 01:29:43 +08:00
libsedml
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linux-foldingathome
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mafft
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mapm3
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megahit
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metaeuk
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migrate
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minimap2
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mmseqs2
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molden
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
mothur
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mrbayes
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mummer
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muscle
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ncbi-blast+
devel/grpc: Update to 1.54.0 (should be part of 8f17596cf5a75f2dca4b4c9f65ba02a53e1b2cd9)
2023-04-20 02:53:02 +08:00
ncbi-cxx-toolkit
graphics/proj: Update to 9.2.0
2023-03-09 13:42:31 +01:00
ncbi-entrez-direct
all: Bump PORTREVISION after lang/go{119,120} update
2023-04-08 10:13:25 -05:00
ncbi-toolkit
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ncbi-vdb
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
ngs-sdk
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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p5-BioPerl-Run
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p5-transdecoder
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p5-TrimGalore
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paml
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pbbam
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pbseqan
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peak-classifier
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
pear-merger
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phrap
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phred
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phyml
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picard-tools
*/*: Refactor java/openjdk7 removal
2023-04-04 13:10:53 -05:00
plink
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
pooler
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primer3
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prodigal
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prodigy-lig
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
protomol
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psi88
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-bcbio-gff
biology/py-bcbio-gff: Update to 0.7.0
2023-03-16 17:32:06 -05:00
py-biom-format
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-biopython
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-biosig
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-bx-python
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-crossmap
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-cutadapt
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py-deeptools
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-deeptoolsintervals
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py-dna-features-viewer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-dnaio
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py-ete3
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
py-Genesis-PyAPI
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py-gffutils
biology/py-gffutils: Update 0.11.0 → 0.11.1
2023-03-12 01:02:31 -08:00
py-goatools
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-gtfparse
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-hits
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py-libnuml
biology/py-libnuml: Allow build with swig 4.1.0+
2023-04-19 02:05:12 +08:00
py-libsedml
biology/py-libsedml: Allow build with swig 4.1.0+
2023-04-19 02:05:12 +08:00
py-loompy
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-macs2
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-mrcfile
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-multiqc
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-ont-fast5-api
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-orange3-bioinformatics
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
py-orange3-single-cell
audio/opus: bump consumers after update to 1.4
2023-04-25 17:17:15 +02:00
py-pandas-charm
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-py2bit
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py-pybigwig
biology/py-pybigwig: Update to 0.3.21
2023-04-01 16:10:15 -05:00
py-pyfaidx
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py-pyrodigal
biology/py-pyrodigal: Update 2.0.3 → 2.1.0
2023-03-19 09:42:53 -07:00
py-pysam
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py-PySCeS
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-python-libsbml
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py-pywgsim
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py-resdk
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-scikit-bio
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
py-valerius
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py-xenaPython
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pyfasta
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
python-nexus
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rainbow
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rampler
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
readseq
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recombine
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rna-seq
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
ruby-bio
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rubygem-bio
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rubygem-bio-executables
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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sam2pairwise
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samtools
biology/samtools: Update to 1.17
2023-02-24 17:27:21 -06:00
scrm
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seaview
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seqan
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seqan1
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seqan3
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
seqan-apps
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seqio
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seqkit
all: Bump PORTREVISION after lang/go{119,120} update
2023-04-08 10:13:25 -05:00
seqtk
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sigviewer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
sim4
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slclust
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smithwaterman
…
snpeff
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spoa
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
sra-tools
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
stacks
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star
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stringtie
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subread
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tabixpp
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taxonkit
biology/taxonkit: Update 0.14.1 → 0.14.2
2023-04-14 22:02:19 -07:00
treekin
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
2023-04-23 09:09:58 +00:00
treepuzzle
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trimadap
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trimmomatic
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tRNAscan-SE
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ucsc-userapps
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ugene
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unikmer
all: Bump PORTREVISION after lang/go{119,120} update
2023-04-08 10:13:25 -05:00
vcf2hap
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vcf-split
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vcflib
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vcftools
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velvet
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viennarna
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vsearch
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vt
…
wfa2-lib
*/*: Sunset 12.3-RELEASE from ports tree
2023-03-30 18:59:51 -05:00
wise
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Makefile
biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics
2023-02-25 08:27:46 -06:00