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Jason W. Bacon 15458dfbac biology/bbmap: BBMap short read aligner, and other bioinformatic tools 
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
2021-04-18 11:21:29 -05:00
..
abyss One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
ad2vcf One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
artemis Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
avida Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
babel all: Remove all other $FreeBSD keywords. 2021-04-06 16:31:13 +02:00
bamtools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bbmap biology/bbmap: BBMap short read aligner, and other bioinformatic tools 2021-04-18 11:21:29 -05:00
bcftools Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
bedtools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bioawk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biococoa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biolibc One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bioparser One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biosoup One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bolt-lmm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bowtie One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bowtie2 biology/bowtie2: Add support for powerpc64le 2021-04-18 10:53:14 -05:00
bwa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
canu One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cd-hit One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cdbfasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
checkm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
clustal-omega One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
clustalw Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
cufflinks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cytoscape One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
ddocent One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
diamond biology/diamond: Update to 2.0.9 2021-04-12 21:55:49 -03:00
dsr-pdb One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
edlib One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
emboss Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
exonerate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fasta3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fastahack One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastdnaml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fastool One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastp One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastqc One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fasttree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastx-toolkit One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
figtree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fluctuate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
freebayes One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
garlic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gatk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gcta One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gemma One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
generand One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gff2ps Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gmap Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gperiodic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
graphlan One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
groopm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
haplohseq One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hhsuite One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hisat2 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hmmer Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
htslib Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
hyphy biology/hyphy: Update to 2.5.30 2021-04-07 22:54:50 -03:00
igv One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
infernal One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
iolib Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
iqtree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
jalview all: Remove all other $FreeBSD keywords. 2021-04-06 16:31:13 +02:00
jellyfish One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
kallisto One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
lamarc Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
libbigwig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libgtextutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libsbml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
linux-foldingathome all: Remove all other $FreeBSD keywords. 2021-04-06 16:31:13 +02:00
mafft Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mapm3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
migrate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
minimap2 biology/minimap2: Update to 2.18 2021-04-11 14:18:02 -05:00
molden Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mopac Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mothur biology/mothur: Update to 1.45.2 2021-04-12 19:29:17 -05:00
mrbayes Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mummer Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
muscle Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ncbi-blast+ One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
ncbi-cxx-toolkit One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
ncbi-toolkit Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ncbi-vdb biology/ncbi-vdb: Restore static libs installed with symlinks as shared libs are usually installed 2021-04-12 11:03:14 -07:00
ngs-sdk biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH 2021-04-15 10:01:31 -07:00
p5-AcePerl Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-ASN1-EntrezGene Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Cluster Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Coordinate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Das Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Das-Lite Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-DB-EMBL Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-DB-NCBIHelper Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-FeatureIO Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-GFF3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Glite Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Graphics Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-MAGETAB Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-NEXUS Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Phylo Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-SCF Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Variation Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-BioPerl Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-BioPerl-Run Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-transdecoder One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
p5-TrimGalore One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
paml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
pbbam One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pbseqan One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pear-merger One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
phrap One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
phred Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
phyml Clean up some things 2021-04-15 10:31:56 +02:00
picard-tools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
plink One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pooler One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
primer3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
prodigal One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
prodigy-lig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
protomol Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
psi88 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-bigwig biology/py-bigwig: Python access to bigWig files using libBigWig 2021-04-12 18:24:20 -05:00
py-biom-format One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-biopython Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-bx-python Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-crossmap biology/py-crossmap: Lift over genomics coordinates between assemblies 2021-04-12 18:37:51 -05:00
py-cutadapt One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-dnaio One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-ete3 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-Genesis-PyAPI One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-gffutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-gtfparse One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-hits One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-loompy One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-macs2 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-multiqc One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-orange3-bioinformatics One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-orange3-single-cell One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pandas-charm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pyfaidx One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pysam One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-scikit-bio One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-xenaPython One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pyfasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
python-nexus Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rainbow One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
rampler One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
readseq biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint 2021-04-18 09:20:28 -05:00
recombine Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ruby-bio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-executables Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-old-biofetch-emulator Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-shell Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
samtools Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
scrm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
seaview Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan-apps Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan1 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqkit biology/seqkit: Change WWW to the project URL (from GitHub URL) 2021-04-16 21:00:56 -07:00
seqtk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
sim4 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
slclust One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
smithwaterman One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
spoa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
stacks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
star One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
stringtie One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
subread One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
tabixpp One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
treekin One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
treepuzzle Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
trimadap One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
trimmomatic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
tRNAscan-SE Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ugene Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
vcf-split One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
vcf2hap One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
vcflib One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
vcftools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
velvet Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
viennarna One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
vsearch biology/vsearch: Update to 2.17.0 2021-04-10 09:02:55 -05:00
vt One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
wise Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
Makefile biology/bbmap: BBMap short read aligner, and other bioinformatic tools 2021-04-18 11:21:29 -05:00