Yuri Victorovich 89f62deb8a biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation		2024-09-20 20:03:29 -07:00
..
abyss	biology/abyss: update 2.3.8 → 2.3.9	2024-09-12 02:18:11 -07:00
ad2vcf
andi	biology/andi: New ports: Efficient estimation of evolutionary distances	2024-09-07 14:31:10 -07:00
artemis
atac-seq
augustus
avida
babel
bamtools	*/*: Bump dependencioes after devel/jsoncpp update	2024-09-12 09:20:06 -07:00
bamutil
barrnap
bbmap
bcf-score
bcftools
bedtools
bfc
bifrost
bio-mocha
bioawk
biococoa
biolibc
biolibc-tools
bioparser
biosig	biology/{.py-}biosig: update 2.6.0 → 2.6.1	2024-08-05 07:37:01 -07:00
biosoup
biostar-tools
bolt-lmm	*/*: Bump PORTVERSION of math/nlopt consumers	2024-08-25 15:33:16 +02:00
bowtie
bowtie2
btllib	biology/btllib: update 1.7.2 → 1.7.3	2024-07-27 13:19:18 -07:00
bwa
canu
cd-hit
cdbfasta
checkm
chip-seq
clustal-omega
clustalw
cufflinks
cytoscape
ddocent
diamond
dsr-pdb
edlib
emboss
erminej
exonerate
fasda
fasta
fasta3
fastahack
fastani	biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation	2024-09-20 20:03:29 -07:00
fastdnaml
fastool
fastp
fastq-trim
fastqc
fasttree
fastx-toolkit
fermi-lite	biology/fermi-lite: Add ONLY_FOR_ARCHS line	2024-09-19 14:05:26 -07:00
figtree
flash
fluctuate
freebayes
garlic
gatk	biology/gatk: Update COMMENT	2024-08-04 13:13:15 -07:00
gcta	biology/gcta: Unbreak fetch	2024-07-08 17:04:44 -05:00
gemma	*/*: bump PORTREVISION after the upgrade to OpenBLAS	2024-06-21 19:49:24 +02:00
generand
gff2ps
gffread
gkl	biology/gkl: New port: Accelerated kernel library for genomics	2024-08-04 13:09:41 -07:00
gmap
gperiodic
graphlan
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to 2.5.62	2024-06-21 13:58:09 -03:00
igv
infernal
iolib
iqtree	biology/iqtree: Update to 2.3.6	2024-09-07 22:53:14 -03:00
jalview
jellyfish
kallisto	biology/kallisto: Update to 0.51.1,1	2024-09-19 17:46:47 -05:00
kmcp	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
lamarc
libbigwig
libcombine
libgff
libgtextutils
libneurosim	devel/automake: Update to 1.17	2024-07-20 13:27:02 +02:00
libnuml
libsbml	biology/libsbml: Update to 5.20.4	2024-09-09 02:36:57 +08:00
libsedml
linux-foldingathome	biology/linux-foldingathome: Point MASTER_SITES to the new location	2024-08-12 14:58:05 +02:00
locarna
mafft
mapm3
mashmap
megahit
metaeuk
migrate	biology/migrate: fix build on !x86	2024-07-09 12:04:31 +02:00
minimap2	biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors	2024-07-20 14:55:08 -05:00
mmseqs2
molden
mothur
mrbayes
mummer
muscle
ncbi-blast+	devel/grpc: Update to 1.66.1	2024-09-16 04:09:34 +08:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.7 → 28.0.8	2024-09-07 21:10:05 -07:00
ncbi-entrez-direct	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
ncbi-toolkit
ncbi-vdb
ngs-sdk
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
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-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore	biology/p5-TrimGalore: Update to 0.6.10	2024-07-23 11:01:28 -04:00
paml
pbbam
peak-classifier
pear-merger
phrap
phred
phyml
picard-tools
plink	*/*: bump PORTREVISION after the upgrade to OpenBLAS	2024-06-21 19:49:24 +02:00
pooler
primer3
prodigal
prodigy-lig
protomol
psi88
py-bcbio-gff
py-biom-format	biology/py-biom-format: update 2.1.10 → 2.1.16	2024-07-13 11:06:57 -07:00
py-biopython
py-biosig	biology/{.py-}biosig: update 2.6.0 → 2.6.1	2024-08-05 07:37:01 -07:00
py-bx-python
py-crossmap
py-cutadapt	biology/py-cutadapt: update to 4.9	2024-06-20 10:38:00 +02:00
py-deeptools
py-deeptoolsintervals
py-dna-features-viewer
py-dnaio	biology/py-dnaio: Update to 1.2.1	2024-07-04 09:15:39 +00:00
py-ete3
py-Genesis-PyAPI
py-gffutils
py-goatools
py-gtfparse
py-hits
py-htseq
py-libnuml
py-libsedml
py-loompy
py-macs2
py-macs3	biology/py-macs3: Update to 3.0.2	2024-09-14 08:23:32 -05:00
py-mrcfile	biology/py-mrcfile: update 1.5.2 → 1.5.3	2024-07-26 01:57:55 -07:00
py-multiqc	devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml	2024-07-07 16:05:33 +08:00
py-newick
py-ont-fast5-api
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-py2bit
py-pybigwig
py-pyfaidx
py-pyrodigal	biology/py-pyrodigal: update 3.5.1 → 3.5.2	2024-09-05 01:48:51 -07:00
py-pysam
py-PySCeS	biology/py-PySCeS: update 1.2.1 → 1.2.2	2024-08-03 01:27:31 -07:00
py-python-libsbml
py-pywgsim
py-resdk	biology/py-resdk: update 21.1.0 → 21.2.0	2024-07-12 01:58:00 -07:00
py-scikit-bio	biology/py-scikit-bio: update 0.6.1 → 0.6.2	2024-07-12 22:17:53 -07:00
py-valerius
py-xenaPython
pyfasta
python-nexus
R-cran-Biobase
R-cran-BiocGenerics
R-cran-BiocManager	biology/R-cran-BiocManager: Update version 1.30.24=>1.30.25	2024-09-08 19:28:55 +02:00
rainbow
rampler
readseq
rna-seq
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon	devel/onetbb: Update to 2021.13.0	2024-07-04 13:39:44 +02:00
sam2pairwise
samtools
scrm
seaview
seqan
seqan1
seqan3
seqan-apps
seqkit	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
seqtk
seqwish
sigviewer
slclust
smithwaterman
snpeff
spoa
sra-tools
stacks
star
stringtie
subread
tabixpp
taxonkit	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps
ugene
unikmer	all: Bump after lang/go121 update	2024-08-09 06:24:08 +00:00
vcf2hap
vcf-split
vcflib
vcftools
velvet
viennarna
vsearch
vt
wfa2-lib	biology/wfa2-lib: fix build without libomp	2024-08-04 14:00:47 +02:00
wise
Makefile	biology/fastani: New port: Fast Whole-Genome Similarity (ANI) Estimation	2024-09-20 20:03:29 -07:00