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Task: Cloud
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
X-Begin-Category: Phylogenetic analysis
Recommends: altree, clearcut, fastdnaml, fasttree, parsinsert, phyml,
phyutility, prime-phylo, mrbayes, tree-puzzle | tree-ppuzzle,
veryfasttree
X-End-Category: Phylogenetic analysis
X-Begin-Category: Genetics and genomics
Recommends: alien-hunter, bagpipe, fastlink, loki, gasic, genometools, plink,
plink1.9, plink2, probabel, r-cran-qtl, r-other-mott-happy.hbrem
X-End-Category: Genetics
X-Begin-Category: Sequence alignments and related programs.
Recommends: amap-align, blast2, biosquid, boxshade, cassiopee, cdbfasta,
cd-hit, clustalo, clustalw, conservation-code, dialign, dialign-tx,
emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch,
embassy-phylip, exonerate, gff2aplot, gff2ps, glam2, gmap, hmmer,
jellyfish, kalign, mafft, mlv-smile, mummer, muscle, muscle3, neobio, poa,
prank, probcons, proda, sibsim4, sigma-align, sim4, snap,
t-coffee, wise
X-End-Category: Sequence alignments and related programs.
X-Begin-Category: High throughput sequencing
Recommends: bamtools, bedtools, flexbar, picard-tools, samtools,
tabix, vcftools
Comment: Processing
Recommends: anfo, cufflinks, bowtie, bowtie2, bwa, last-align, maq, perm,
hisat2, smalt, soapdenovo, soapdenovo2
Comment: Aligners
Recommends: abyss, mapsembler2, idba, minia, mira-assembler, ssake, velvet
Comment: Assembly
Recommends: ampliconnoise, arden, fastqc
Comment: Filtering and QC
Recommends: discosnp, dnaclust, fitgcp, giira, grinder, kissplice, macs,
mothur, paraclu, r-bioc-hilbertvis, sra-toolkit
Comment: Other
X-End-Category: High throughput sequencing
X-Begin-Category: Analysis of RNA sequences.
Recommends: aragorn, infernal, rnahybrid, rtax
X-End-Category: Analysis of RNA sequences.
X-Begin-Category: Molecular modelling and molecular dynamics
Recommends: autodock, autodock-vina, autogrid, concavity, dssp, freecontact,
gromacs, hhsuite, mustang, pdb2pqr, raster3d, theseus
Comment: non-free
X-End-Category: Molecular modelling and molecular dynamics
X-Begin-Category: Tools for the molecular biologist.
Recommends: melting, mipe, ncbi-epcr, primer3
Comment: Oligonucleotides and PCR
Recommends: acedb-other, disulfinder, ncbi-tools-bin, ncoils,
readseq, tigr-glimmer, seqan-apps, staden-io-lib-utils
Recommends: python3-cogent3
X-End-Category: Tools for the molecular biologist.
X-Begin-Category: Others
Recommends: aevol, python3-biomaj3-cli, bioperl, bioperl-run,
clonalframe, circos, datamash, prodigal,
python3-biopython, qiime, r-bioc-edger, r-cran-pvclust,
r-cran-vegan
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