Bioinformatics | Abricate, Abyss, Abyss-mpi, AdapterRemoval, AfterQC, Aligngraph, AlleleSeq, Allpathslg, AmrPlusPlus, AnnotSV, AnnotSV, Annovar, Aragorn, armatus, Artemis, ArtificialFastqGenerator, Augustus, bam-readcount, Bambamc, Bamtools, bamUtil, barrnap, BASE, Basespace, BatMeth, BayesAss, Bbmap, BCFtools, Bcl2fastq, Beagle, Beast, BEDOPS, Bedtools, biobambam2, Biopieces, Bismark, Blasr, Blast, BLAST+, Blat, BlobTools, Bowtie, Bowtie2, bpp, Bracken, BRAKER1, BRAKER2, Brig, Busco, Bvatools, BWA, CAFExp, Canu, Cap3, CCMetagen, Cd-Hit, Cell Ranger, Centrifuge, Chimera, Chimeraslayer, ChunkChromosome, ClinSV, Clonalframeml, Clustal Omega, Clustal W/X, CNVnator, Codonphyml, coevol, Cortex, Crest, Cufflinks, Cutadapt, Delly, DETONATE, Diamond, Drive5, dx-toolkit, Ea-Utils, EDirect, EffectorP, Emboss, EMMAX, EPA-ng, Epacts, EVidenceModeler, ExaBayes, EXCAVATOR2tool, exonerate, Falcon, Falcon-Unzip, FastME, Fastml, fastp, fastPHASE, FastQC, fastQValidator, Fasttree, Fastx, fgbio, FImpute, Flash, fqgrep, fqtools, FragGeneScan, FRANz, freebayes, funannotate, FUSTr, gatb, Gatk, Gblocks, gcta, gem-tools, Gemma, GeneMark-ES, Genomemasker, GenomeTools, Gess, giremi, gmap, GPS-Lipid, GraPhlAn, GraPhlAn, GRIDSS, GTFTools, Gubbins, Haddock, hapcut, Hapcut, Hapflow, haplotyper, Haploview, Hapsembler, Hh-Suite, HiC-bench, HiCUP, HISAT2, hlascan, hmftools, Hmmer, Homer, hotspotter, HTSlib, I-Tasser, Idba, idp, Igvtools, IMPUTE2, Infernal, InterProScan, IQ-TREE, Is_Mapper, ITSx, Iva, Jaspa, Jellyfish, Juicer, Kalign, kallisto, Kat, kentutils, KMA, Kmc, KohGPI, Kraken, Kraken2, KronaTools, kSNP, LAST, LASTZ, libmaus2, lighter, Lofreq, longranger, lordec, lumpy-sv, MACH, MaCH-Admix, MAFFT, Magic-BLAST, Maker, Manta, MARVEL, Mash, MATAM, Mauve, MaxBin2, Medusa, Megacc, Megahit, megan, MELT, Meme, MetaBAT, MetaPhlAn2, MetaSim, Metatissue, MetaVelvet, meth_progs, Methpipe, MethylDackel, Migrate-N, minced, Minimac2, Minimac4, Minimap2, Mira, Mirdeep2, MISTReSS, Mlst, Mothur, mpiBWA, Mrbayes, Mugsy, Mummer3, Mummer4, Mutect, Mykrobe-Predictor, NanoOk, Nanopolish, NCBI C++ Toolkit, Newick-Utils, Norgal, Nullarbor, oases, OmegaPlus, OrthoFiller, OrthoFinder, Paml, pandaseq, Pblat, Pear, PennCNV, pgdspider, phase, Pheniqs, Phobius, PHYLIP, PhyloBayes, Phyml, Picard, Pilon, Pindel, Pipits, Platypus, PLINK, PneumoCaT, PneumoCaT, pplacer, Prank, Preseq, Prinseq, Prodigal, Prokka, ProteinOrtho, PSIPRED, PSMC, Purge Haplotigs, Qiime, Qorts, Qualimap, QUAST, QuickTree, Racon, Ragout, RAiSD, Ray, Rdpclassifier, Readseq, REAPR, Reddog, Repeatmasker, Repeatmodeler, RepeatScout, Rmats, Rnammer, Roary, Rosetta, RSEM, Salmon, sam2bam, Sambamba, Samblaster, samclip, Samtools, scotti, SecretomeP, selscan, SeqKit, seqOutBias, Seqtk, sff2fastq, Sga, SHAPEIT, Shorah, ShortStack, shovill, Sibelia, Signalp, SiLiX, SKESA, SLiMSuite, Smalt, SMRT, SMRTtools, SNAP, Snippy, snp-dists, SNP-sites, SnpEff, SNPhylo, SOAPdenovo2, SortMeRNA, Spades, SpeedSeq, Sratoolkit, STACKS, Stampy, Star, Strainseeker, Strelka, Stringtie, subread, Subread, Supernova, Surpi, Svtyper, sweed, SweepFinder2, SynerClust, Tabix, tantan, taxator-tk, Tbl2Asn, Tophat, Tracer, Transdecoder, Trim Galore, trimAl, Trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Genome Browser, Usearch, UVP, Varscan, VaST, vcf2diploid, Vcftools, Velvet, VelvetOptimiser, ViennaRNA, Vmatch, Vsearch, WALT, Wgs, wgsim, XHMM, XP-EHH |
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Code Development Utilities | Anaconda, Anaconda2, Argtable2, Bazel, Binutils, Bison, Cmake, Dbus, Dbus-Glib, Doxygen, emacs, Expat, Flex, Fontconfig, Gdl, Gflags, Git, Glib, Graphviz, Guile, Icmake, Icu, Jupyter, Leveldb, Libcroco, Libcurl, Libffi, Libgc, Libmng, Libspatialite, Libspectre, Libtau, Libtiff, Libtool, Libxml2, Libxslt, Luabind, Luajit, Maven, Mercurial, Ncurses, Node, Pango, Pcre, Pcre2, Protobuf, Raxml, Raxmls, Scons, Slang, Sparsehash, Spatialite, Sphinx, Subversion, Swig, tre, Udunits, Vcflib, Xmlto, Yasm |
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