Jason W. Bacon 364ffe7adb biology/vsearch: Update to 2.15.0 ... Numerous minor enhancements		2020-06-20 14:31:59 +00:00
..
abyss	biology/abyss: Update 2.2.3 -> 2.2.4	2020-05-30 09:10:44 +00:00
artemis
avida
babel
bamtools
bcftools
bedtools
bioawk	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00
biococoa
bolt-lmm
bowtie
bowtie2
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
cytoscape
ddocent
diamond	biology/diamond: Update to version 0.9.34	2020-06-12 12:12:12 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk	biology/gatk: Update 4.1.5.0 -> 4.1.7.0	2020-05-28 02:26:51 +00:00
gcta
gemma
gff2ps
gmap
gperiodic
graphlan
grappa
groopm
haplohseq
hhsuite
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.5.14	2020-05-30 19:39:11 +00:00
igv
infernal
iolib
iqtree	biology/iqtree: Update to version 2.0.6	2020-05-30 18:43:26 +00:00
jalview
jellyfish
kallisto
lagan
lamarc
libbigwig
libgtextutils
libsbml	Move devel/swig30 to devel/swig and update to 4.0.1	2020-06-17 18:17:45 +00:00
linux-foldingathome
mafft
mapm3
migrate
minimap2
molden
mopac
mothur
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit
ncbi-toolkit
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
paml
pbbam
pbcopper
pbseqan
pear-merger
phrap	Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).	2020-05-27 11:59:13 +00:00
phred
phylip
phyml
picard-tools	biology/picard-tools: CLI tools for manipulating sequencing data	2020-06-13 13:54:47 +00:00
plink
primer3
prodigal
prodigy-lig	Unbreak bulk -a	2020-06-13 15:05:44 +00:00
protomol
psi88
py-biom-format
py-biopython	biology/py-biopython: Set python requirement to 3.6+	2020-06-13 13:42:12 +00:00
py-bx-python
py-cutadapt
py-dnaio
py-ete3
py-fastTSNE
py-Genesis-PyAPI
py-gffutils	biology/py-gffutils: Update 0.10 -> 0.10.1	2020-06-16 02:10:08 +00:00
py-gtfparse
py-hits
py-loompy	biology/py-loompy: Update 2.0.17 -> 3.0.6	2020-06-16 02:26:08 +00:00
py-macs2
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm	Clean up some things	2020-05-30 00:57:02 +00:00
py-pyfaidx
py-pysam	biology/py-pysam: Update 0.15.4 -> 0.16.0	2020-06-09 05:03:48 +00:00
py-scikit-bio
py-xenaPython
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
scrm
seaview	biology/seaview: Update version 5.0.2=>5.0.3	2020-06-14 09:24:18 +00:00
seqan
seqan1
seqan-apps
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star
stringtie
subread	biology/subread: Read alignment, quantification and mutation discovery	2020-06-05 01:55:49 +00:00
tabixpp
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
vcflib
vcftools
velvet
viennarna
vsearch	biology/vsearch: Update to 2.15.0	2020-06-20 14:31:59 +00:00
vt	Add compiler:c++0x to USES to fix build on GCC-based systems:	2020-06-05 03:49:53 +00:00
wise
Makefile	biology/picard-tools: CLI tools for manipulating sequencing data	2020-06-13 13:54:47 +00:00