deb_control_files:
- control
- md5sums
- postinst
- prerm
deb_fields:
Architecture: all
Depends: med-config (= 3.8.1), med-tasks (= 3.8.1)
Description: |-
Debian Med bioinformatics packages
This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
Installed-Size: '44'
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Package: med-bio
Priority: optional
Recommends: abacas, abpoa, abyss, acedb-other, adapterremoval, adun-core, aegean,
aevol, alien-hunter, alter-sequence-alignment, altree, amap-align, ampliconnoise,
andi, any2fasta, aragorn, arden, ariba, art-nextgen-simulation-tools, artemis,
artfastqgenerator, assembly-stats, assemblytics, atac, ataqv, atropos, augur,
augustus, autodock, autodock-vina, autogrid, avogadro, axe-demultiplexer, baitfisher,
bali-phy, ballview, bamclipper, bamkit, bamtools, bandage, barrnap, bbmap, bcalm,
bcftools, beads, beagle, beast-mcmc, beast2-mcmc, bedops, bedtools, belvu, berkeley-express,
bio-eagle, bio-rainbow, bio-tradis, bio-vcf, bioawk, biobambam2, biosyntax, bitseq,
blasr, blixem, bolt-lmm, bowtie, bowtie2, boxshade, bppphyview, bppsuite, brig,
btllib-tools, busco, bustools, bwa, canu, cassiopee, cat-bat, cct, cd-hit, cdbfasta,
centrifuge, cgview, changeo, chimeraslayer, chromhmm, chromimpute, cif-tools,
circlator, circos, clearcut, clonalframe, clonalframeml, clonalorigin, clustalo,
clustalw, clustalx, cnvkit, codonw, comet-ms, concavity, conservation-code, covtobed,
crac, csb, cutadapt, cutesv, daligner, damapper, datamash, dawg, dazzdb, delly,
density-fitness, dextractor, dialign, dialign-tx, diamond-aligner, discosnp, disulfinder,
dnaclust, dnarrange, dotter, drop-seq-tools, dssp, dwgsim, e-mem, ea-utils, ecopcr,
edtsurf, eigensoft, elph, embassy-domainatrix, embassy-domalign, embassy-domsearch,
emboss, emmax, estscan, examl, exonerate, fasta3, fastahack, fastani, fastaq,
fastdnaml, fastlink, fastml, fastp, fastq-pair, fastqc, fastqtl, fasttree, ffindex,
figtree, filtlong, fitgcp, flash, flexbar, flye, fml-asm, freebayes, freecontact,
fsa, fsm-lite, gamgi, garli, garlic, gasic, gatb-core, gbrowse, gdpc, gemma, genometester,
genomethreader, genometools, genomicsdb-tools, gentle, gff2aplot, gff2ps, gffread,
ggd-utils, ghemical, ghmm, glam2, gmap, grabix, graphlan, grinder, gromacs, gsort,
gubbins, gwama, harvest-tools, hhsuite, hilive, hinge, hisat2, hmmer, hmmer2,
hyphy-mpi | hyphy-pt, idba, igblast, igor, igv, indelible, infernal, insilicoseq,
ipig, iqtree, iva, jaligner, jalview, jellyfish, jellyfish1, jmodeltest, jmol,
kalign, kallisto, kaptive, khmer, kineticstools, king-probe, kissplice, kleborate,
kma, kmc, kmer, kmerresistance, kraken, kraken2, lagan, lamarc, lamassemble, lambda-align,
lambda-align2, last-align, lastz, leaff, lefse, libpwiz-tools, librg-utils-perl,
libvcflib-tools, lighter, logol, loki, ltrsift, lucy, lumpy-sv, macs, macsyfinder,
maffilter, mafft, malt, mapdamage, mapsembler2, maq, maqview, mash, massxpert,
mauve-aligner, mcaller, mecat2, megadepth, megahit, megan-ce, melting, meryl,
metabat, metaphlan, metastudent, mhap, microbegps, microbiomeutil, mindthegap,
minexpert2, minia, miniasm, minimac4, minimap, minimap2, mipe, mira-assembler,
mirtop, mlv-smile, mmb, mmseqs2, mosdepth, mothur, mptp, mrbayes, multiqc, mummer,
murasaki | murasaki-mpi, muscle, muscle3, mustang, nanofilt, nanolyse, nanook,
nanopolish, nanostat, nanosv, nast-ier, ncbi-acc-download, ncbi-blast+, ncbi-blast+-legacy,
ncbi-entrez-direct, ncbi-epcr, ncbi-seg, ncbi-tools-bin, ncbi-tools-x11, ncl-tools,
ncoils, neobio, ngmlr, njplot, norsnet, norsp, ntcard, nxtrim, obitools, openms,
optimir, pal2nal, paleomix, paml, paraclu, parasail, parsinsert, parsnp, patman,
pbdagcon, pbhoney, pbjelly, pbsim, pbsuite, pdb2pqr, perlprimer, perm, pftools,
phast, phipack, phybin, phylip, phylonium, phyml, physamp, phyutility, phyx, picard-tools,
picopore, pigx-rnaseq, piler, pilercr, pilon, pinfish, pique, pirs, pizzly, placnet,
plasmidid, plasmidomics, plasmidseeker, plast, plink, plink1.9, plink2, plip,
poa, populations, porechop, poretools, prank, predictnls, presto, prime-phylo,
primer3, prinseq-lite, proalign, probabel, probalign, probcons, proda, prodigal,
profbval, profisis, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md,
profnet-norsnet, profnet-prof, profnet-snapfun, profphd-net, profphd-utils, proftmb,
progressivemauve, prokka, proteinortho, prottest, provean, pscan-chip, pscan-tfbs,
psortb, pullseq, pycoqc, pycorrfit, pyensembl, pyfastx, pymol, pyscanfcs, python3-biomaj3-daemon,
python3-cogent3, python3-emperor, python3-geneimpacts, python3-gffutils, python3-pairtools,
python3-pybedtools, python3-sqt, python3-treetime, pyvcf, qcat, qcumber, qiime,
qtltools, quicktree, quorum, qutemol, r-bioc-annotate, r-bioc-biostrings, r-bioc-cner,
r-bioc-cummerbund, r-bioc-deseq2, r-bioc-ebseq, r-bioc-edger, r-bioc-genefilter,
r-bioc-geoquery, r-bioc-hilbertvis, r-bioc-htsfilter, r-bioc-impute, r-bioc-limma,
r-bioc-megadepth, r-bioc-mergeomics, r-bioc-metagenomeseq, r-bioc-mofa, r-bioc-multiassayexperiment,
r-bioc-mutationalpatterns, r-bioc-pcamethods, r-bioc-phyloseq, r-bioc-rtracklayer,
r-bioc-scater, r-bioc-tfbstools, r-cran-adegenet, r-cran-adephylo, r-cran-alakazam,
r-cran-ape, r-cran-bio3d, r-cran-distory, r-cran-genabel, r-cran-kaos, r-cran-metamix,
r-cran-phangorn, r-cran-phytools, r-cran-pscbs, r-cran-qtl, r-cran-rotl, r-cran-samr,
r-cran-sdmtools, r-cran-seqinr, r-cran-seurat, r-cran-shazam, r-cran-spp, r-cran-tcr,
r-cran-tigger, r-cran-treescape, r-cran-tsne, r-cran-vegan, r-cran-webgestaltr,
r-cran-wgcna, r-other-ascat, r-other-mott-happy.hbrem, r-other-rajewsky-dropbead,
racon, radiant, ragout, rambo-k, rampler, rapmap, rasmol, raster3d, rate4site,
raxml, ray, rdp-alignment, rdp-classifier, rdp-readseq, readseq, readucks, reapr,
recan, relion, relion-gui, repeatmasker-recon, reprof, resfinder, rna-star, rnahybrid,
roary, rockhopper, roguenarok, rsem, rtax, runcircos-gui, saint, salmid, salmon,
sambamba, samblaster, samclip, samtools, savvy-util, scoary, scrappie, scrm, scythe,
seaview, seer, segemehl, seqan-apps, seqan-needle, seqan-raptor, seqkit, seqmagick,
seqprep, seqsero, seqtk, sga, shasta, shovill, sibelia, sibsim4, sickle, sigma-align,
sim4, sim4db, simka, simkamin, ska, skesa, skewer, smalt, smithwaterman, smrtanalysis,
snap, snap-aligner, sniffles, snp-sites, snpeff, snpomatic, snpsift, soapaligner,
soapdenovo, soapdenovo2, soapsnp, sortmerna, spaced, spades, spaln, spoa, sprai,
spread-phy, squizz, sra-toolkit, srst2, ssake, sspace, ssw-align, stacks, staden,
staden-io-lib-utils, stringtie, subread, suitename, sumaclust, sumatra, sumtrees,
surankco, surpyvor, survivor, svim, swarm, sweed, t-coffee, tabix, tantan, terraphast,
theseus, thesias, tiddit, tigr-glimmer, tm-align, tnseq-transit, toil, tombo,
tophat-recondition, topp, toppred, tortoize, trace2dbest, tracetuner, transdecoder,
transrate-tools, transtermhp, tree-puzzle | tree-ppuzzle, treeview, treeviewx,
trf, trim-galore, trimmomatic, tvc, twopaco, uc-echo, umap-learn, umis, uncalled,
unicycler, unikmer, varna, vcfanno, vcftools, velvet | velvet-long, velvetoptimiser,
virulencefinder, vmatch, vsearch, vt, wham-align, wigeon, wise, xpore, yaha, yanagiba,
yanosim
Section: metapackages
Source: debian-med
Suggests: acacia, adun.app, agat, amos-assembler, amoscmp, anfo, annovar, apollo,
arachne, arb, arvados, asap, axparafit, axpcoords, bagpipe, bambus, bax2bam, bcbio,
biceps, big-blast, bigsdb, bismark, blat, blimps-utils, blobology, braker, btk-core,
cactus, caftools, card-rgi, catfishq, cdna-db, cellprofiler, cinema, cluster3,
cmap, conda-package-handling, condetri, contrafold, contralign, coot, copycat,
covpipe, crossbow, crux-toolkit, cufflinks, cytoscape, dascrubber, dazzle, deepbinner,
deepnano, dendroscope, diann, dnapi, e-hive, ecell, embassy-phylip, emboss-explorer,
ensembl, ensembl-vep, epigrass, estferret, euler-sr, euler2, exabayes, exalt,
excavator, ffp, fieldbioinformatics, figaro, flappie, forester, forge, galaxy,
gatk, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gerp++,
getdata, glimmerhmm, gmv, gramalign, graphbin, graphmap2, haploview, hawkeye,
htqc, hts-nim-tools, idefix, idseq-bench, igdiscover, illustrate, inspect, jbrowse,
jigsaw, kempbasu, libhdf5-dev, libhnswlib-dev, lofreq, mach-haplotyper, mage2tab,
maker2, manta, marginphase, martj, maude, maxd, medaka, meme, mesquite, metabit,
metaeuk, metarep, metastudent-data, metastudent-data-2, migrate, minimus, mirbase,
modeller, molekel, mosaik-aligner, mpsqed, mrs, msatfinder, mugsy, mummergpu,
mview, nano-snakemake, nanocall, nanocomp, nanoplot, ncbi-magicblast, nextsv,
ngila, ngsqctoolkit, nw-align, oases, obo-edit, oligoarrayaux, omegamap, oncofuse,
operondb, optitype, paipline, pangolin, partigene, partitionfinder, patristic,
pcma, pfaat, phagefinder, phpphylotree, phylographer, phylophlan, phyloviz-core,
phylowin, pigx-scrnaseq, pipasic, plato, pomoxis, pplacer, profit, profphd, prot4est,
psipred, pssh2, pufferfish, purple, pyrophosphate-tools, python3-alignlib, python3-anndata,
python3-cgecore, python3-cyvcf2, python3-deeptools, python3-deeptoolsintervals,
python3-htseq, python3-intake, python3-loompy, python3-nanoget, python3-nanomath,
python3-ncls, python3-orange, python3-py2bit, python3-pybel, python3-pychopper,
python3-pyfaidx, python3-pyflow, python3-pyranges, python3-pyrle, python3-pysam,
python3-tinyalign, q2-alignment, q2-composition, q2-cutadapt, q2-dada2, q2-deblur,
q2-demux, q2-diversity, q2-emperor, q2-feature-classifier, q2-feature-table, q2-fragment-insertion,
q2-gneiss, q2-longitudinal, q2-metadata, q2-phylogeny, q2-quality-control, q2-quality-filter,
q2-sample-classifier, q2-taxa, q2-types, q2-vsearch, q2cli, q2templates, qtlcart,
qtlreaper, qualimap, quast, r-bioc-annotationhub, r-bioc-aroma.light, r-bioc-beachmat,
r-bioc-biocneighbors, r-bioc-biocsingular, r-bioc-bitseq, r-bioc-ctc, r-bioc-dnacopy,
r-bioc-ensembldb, r-bioc-experimenthub, r-bioc-geneplotter, r-bioc-genomicalignments,
r-bioc-genomicfiles, r-bioc-genomicranges, r-bioc-go.db, r-bioc-grohmm, r-bioc-gviz,
r-bioc-isoformswitchanalyzer, r-bioc-mofa2, r-bioc-org.hs.eg.db, r-bioc-org.mm.eg.db,
r-bioc-qusage, r-bioc-savr, r-bioc-singlecellexperiment, r-bioc-structuralvariantannotation,
r-bioc-tximport, r-cran-amap, r-cran-biwt, r-cran-boolnet, r-cran-corrplot, r-cran-drinsight,
r-cran-dynamictreecut, r-cran-epir, r-cran-fitdistrplus, r-cran-forecast, r-cran-gprofiler2,
r-cran-minerva, r-cran-optimalcutpoints, r-cran-parmigene, r-cran-pheatmap, r-cran-qqman,
r-cran-rcpphnsw, r-cran-rentrez, r-cran-sctransform, r-other-apmswapp, r-other-fastbaps,
raccoon, raxml-ng, rbs-finder, relion-cuda, relion-gui-cuda, repeatmasker, resfinder-db,
roadtrips, roche454ace2caf, rosa, rose, rsat, sailfish, sap, science-workflow,
sepp, seq-gen, seq-seq-pan, seqcluster, seqwish, sift, signalalign, sina, sistr,
situs, snippy, solvate, sourmash, sparta, splitstree, ssaha, strap, strap-base,
strelka, tab2mage, tacg, tandem-genotypes, taverna, taxinspector, tetra, tide,
tigr-glimmer-mg, tipp, tn-seqexplorer, tophat, treebuilder3d, trinityrnaseq, tripal,
trnascan-se, twain, ufasta, ugene, umap, unc-fish, uniprime, varmatch, varscan,
vdjtools, vg, vienna-rna, viewmol, vmd, x-tandem-pipeline, zodiac-zeden
Version: 3.8.1
srcpkg_name: debian-med
srcpkg_version: 3.8.1