Re: Bio-Linux vs Debian-Med package lists

[Andreas Tille <andreas@fam-tille.de>]

Hi Tony,

no idea why your mail did not made it to the list - I'm answering
to what I've bounced here.

On Sun, Feb 11, 2018 at 09:46:50AM +0100, Tony Travis wrote:
> I've compared our Bio-Linux 'master' package list used to create the
> 'live/install' USB stick with your "med-bio*" list of 'Recommends:'.

Thanks for the comparison.  Could you do me some favour and either push
these two lists to some public space or do some

   sed -i 's/^bio-linux-//'  bl_master_package_list.txt

before the diff.  There are quite a lot of bio-linux- prefixed packages
which are available in Debian and spoil the comfortable reading of that
list.

Thanks a lot

      Andreas.

> --- bl_master_package_list.txt	2018-02-10 16:00:10.884359198 +0100
> +++ debian-med-bio.list	2018-02-10 16:18:37.468326503 +0100
> @@ -1,357 +1,559 @@
> +
> +abacas
>  abyss
>  acacia
> +acedb-other
> +adapterremoval
> +adun-core
> +aegean
> +aevol
> +alien-hunter
> +alter-sequence-alignment
> +amap-align
> +amos-assembler,
> +amoscmp
>  ampliconnoise
> -apache2
> -beam2
> -bio-linux-ampliconnoise
> -bio-linux-archaeopteryx
> -bio-linux-artemis
> -bio-linux-assembly-conversion-tools
> -bio-linux-backups
> -bio-linux-big-blast
> -bio-linux-blast
> -bio-linux-bldp-files
> -bio-linux-blixem
> -bio-linux-cap3
> -bio-linux-catchall
> -bio-linux-cd-hit
> -bio-linux-clustal
> -bio-linux-cytoscape
> -bio-linux-dendroscope
> -bio-linux-dotter
> -bio-linux-dust
> -bio-linux-emboss
> -bio-linux-fasta
> -bio-linux-fastdnaml
> -bio-linux-fastqc
> -bio-linux-fasttree
> -bio-linux-gap2caf
> -bio-linux-glimmer3
> -bio-linux-happy:i386
> -bio-linux-hmmer
> -bio-linux-jmotu
> -bio-linux-jprofilegrid
> -bio-linux-keyring
> -bio-linux-lucy
> -bio-linux-mate-desktop
> -bio-linux-mcl
> -bio-linux-mesquite
> -bio-linux-mira
> -bio-linux-mira-3rd-party
> -bio-linux-mothur
> -bio-linux-mrbayes
> -bio-linux-msatfinder
> -bio-linux-mspcrunch
> -bio-linux-mummer
> -bio-linux-muscle
> -bio-linux-mview
> -bio-linux-ncbi-tools-x11
> -bio-linux-njplot
> -bio-linux-nrdb
> -bio-linux-ocount
> -bio-linux-oligoarray
> -bio-linux-oligoarrayaux
> -bio-linux-omegamap
> -bio-linux-paml
> -bio-linux-pfaat
> -bio-linux-phylip
> -bio-linux-phyml
> -bio-linux-priam
> -bio-linux-primer3
> -bio-linux-qiime
> -bio-linux-qtlcart
> -bio-linux-rasmol
> -bio-linux-rbs-finder
> -bio-linux-rdp-classifier
> -bio-linux-readseq
> -bio-linux-sampledata
> -bio-linux-samtools
> -bio-linux-splitstree
> -bio-linux-squint
> -bio-linux-staden
> -bio-linux-stars
> -bio-linux-tablet
> -bio-linux-taxinspector
> -bio-linux-t-coffee
> -bio-linux-tetra
> -bio-linux-themes-v8
> -bio-linux-tree-puzzle
> -bio-linux-treeview
> -bio-linux-tutorials
> -bio-linux-usb-maker
> -bio-linux-xcut
> -bio-linux-zsh
> -bioperl
> -bioperl-run
> +andi
> +apollo
> +arachne
> +aragorn
> +arb
> +ariba
> +artemis
> +asap
> +atac
> +augustus
> +autodock
> +autodocktools,
> +autodock-vina
> +autogrid
> +avogadro,
> +axe-demultiplexer
> +axparafit,
> +bagpipe
> +baitfisher
> +ballview
> +bambus
> +bandage
> +barrnap
> +beads
> +beagle
> +beast-mcmc
> +beast-mcmc,
> +bedops
> +biceps
> +big-blast
> +bigsdb
> +bioclipse
> +bio-eagle
> +bioperl,
>  biosquid
> +bitseq
> +blasr
> +blat
>  blimps-utils
> -bowtie
> -bowtie2
> -bowtie2-examples
> -bowtie-examples
> +blixem,
> +blobology
> +bowtie,
> +boxshade,
> +bppsuite,
> +btk-core
>  bwa
> +cactus
> +caftools
> +card-rgi
> +cassiopee
> +ccs
>  cdbfasta
> -chimeraslayer
> -chkrootkit
> -cifs-utils
> -cmake
> -cufflinks
> -curl
> -cython
> -cython-dbg
> -debconf
> -default-jdk
> -dialign
> -dictionaries-common
> -eclipse
> -emacs
> -emacsen-common
> -emacs-goodies-el
> -estscan2
> -evince
> -evolution
> -evolution-indicator
> -fastdnaml
> -fastjar
> +cd-hit
> +cdna-db
> +cellprofiler
> +centrifuge
> +cgview,
> +cinema
> +circlator
> +circos,
> +clearcut
> +clonalframe,
> +clonalorigin
> +clustalx
> +clustalx,
> +cluster3
> +cmap
> +cnvkit
> +codonw
> +compclust
> +concavity
> +condetri
> +conservation-code
> +contrafold
> +contralign
> +coot
> +copycat
> +crossbow
> +crux-toolkit
> +csb
> +cytoscape
> +daligner
> +das-proserver
> +dawg
> +dazzdb
> +dazzle
> +decipher
> +diamond-aligner
> +discosnp
> +discosnp,
> +disulfinder
> +dssp
> +ecell
> +ecopcr
> +edtsurf
> +e-hive
> +eigensoft
> +elph
> +embassy-domalign,
> +emboss
> +emmax
> +emperor
> +ensembl
> +est-db
> +estferret
> +estscan
> +euler2,
> +exabayes
> +exalt
> +examl,
> +excavator
> +falcon
> +fasta
> +fasta3
> +fastahack
> +fastlink,
> +fastml
> +fastqtl
> +fasttree
>  fastx-toolkit
> -g++
> -galaxy-server-all
> -gcc
> -gedit
> -gfortran
> -gimp
> +ffindex
> +ffp
> +figaro
> +finex
> +fitgcp
> +freebayes
> +freecontact
> +fsa
> +galaxy
> +garli
> +gasic
> +gassst
> +gatb-core
> +gatk
> +gbrowse
> +gbrowse-syn
> +genemark
> +genesplicer
> +genetrack
> +genezilla
> +genographer
> +genometools
> +gentle
> +gff2ps,
>  glam2
> -gnome-session-fallback*
> -gnuplot
> -graphicsmagick
> -graphviz
> -hmmer
> -hyphy
> -icedtea-7-plugin
> -indicator-applet-complete
> +glimmerhmm
> +gmv
> +grabix
> +graphlan
> +gromacs
> +gubbins
> +gwama
> +haploview
> +harvest-tools
> +hexamer
> +hhsuite
> +hilbertvisgui
> +hmmer2
> +htqc
> +hyphygui,
> +indelible
> +infernal
> +ipig
> +jaligner
>  jalview
> +jbrowse
>  jellyfish
> -jemboss
> -last-align
> -lastz
> -less
> -libapache2-reload-perl
> -libapache-dbi-perl
> -libbiojava-java
> -libbiojava-java-demos
> -libc6-dev
> -libconfig-simple-perl
> -libdata-stag-perl
> -libdbd-pg-perl
> -libio-string-perl
> -libmailtools-perl
> -libspreadsheet-parseexcel-perl
> -libspreadsheet-writeexcel-perl
> -libtext-csv-perl
> -lynx
> +jigsaw
> +kempbasu
> +kineticstools
> +king-probe
> +kmc
> +kmer
> +lagan
> +lamarc
> +lambda-align
> +leaff
> +lefse
> +libace-perl
> +libai-fann-perl
> +libbambamc-dev
> +libbamtools-dev
> +libbiococoa-dev
> +libbio-das-lite-perl
> +libbiod-dev
> +libbio-eutilities-perl
> +libbio-graphics-perl,
> +libbiojava-java,
> +libbio-mage-perl
> +libbio-mage-utils-perl
> +libbio-primerdesigner-perl
> +libbpp-core-dev,
> +libchado-perl
> +libdivsufsort-dev
> +libfast5-dev,
> +libfastahack-dev
> +libffindex0-dev
> +libfml-dev
> +libforester-java
> +libfreecontact-dev,
> +libgatbcore-dev
> +libgenome-1.3-dev,
> +libgenome-perl,
> +libgenometools0-dev
> +libgff-dev
> +libgff-perl
> +libgkarrays-dev
> +libgoby-java
> +libgo-perl
> +libhmsbeagle-dev
> +libhts-dev
> +libhtsjdk-java
> +libjebl2-java
> +libjloda-java
> +libkmer-dev
> +libminimap-dev
> +libncl-dev
> +libngs-sdk-dev,
> +libnhgri-blastall-perl
> +libopenms-dev
> +libpal-java
> +libpbbam-dev
> +libpbseq-dev,
> +libqcpp-dev
> +libqes-dev
> +librdp-taxonomy-tree-java
> +librelion-dev
> +librg-blast-parser-perl
> +librg-reprof-bundle-perl
> +librg-utils-perl
> +libroadrunner-dev,
> +librostlab3-dev
> +librostlab-blast0-dev
> +libsbml5-dev,
> +libseqlib-dev
> +libsmithwaterman-dev
> +libsnp-sites1-dev
> +libsort-key-top-perl
> +libsrf-dev
> +libssm-dev
> +libssw-dev,
> +libstaden-read-dev
> +libswiss-perl
> +libtabixpp-dev
> +libtfbs-perl
> +libvcflib-dev
> +libvibrant6-dev
> +libzerg0-dev,
> +lofreq
> +logol-bin
> +ltrsift
> +lucy
> +mach-haplotyper
> +macsyfinder
> +maffilter
>  mafft
> -make
> -maq
> +mage2tab,
> +maker2
> +malt
> +manta
> +mapsembler2
> +martj
> +mash
> +mauve-aligner
> +maxd
>  mcl
> -mdadm
> -meld
> +melting
>  meme
> -meme-examples
> +meryl
> +mesquite
> +metabit
> +metaphlan2
> +metarep
> +metastudent
> +mgltools-networkeditor,
> +mhap
> +microbegps
>  microbiomeutil
> -mira-3rdparty
> -mira-assembler
> -mira-doc
> -mira-examples
> +microbiomeutil,
> +migrate
> +minia
> +miniasm
> +minimap
> +minimus
> +mipe
> +mirbase
> +mlv-smile
> +modeller
> +molekel
>  mothur
> -mrbayes
> -mummer
> +mothur,
> +mpsqed
> +mptp
> +msatfinder
> +mugsy
> +mummer,
> +mummergpu
> +murasaki
>  muscle
> -mysql-client
> -ncbi-tools-bin
> -njplot
> -openjdk-7-jdk
> -openjdk-7-jre
> -openmpi-bin
> -openmpi-common
> -openssh-server
> -oswitch
> +mview
> +nanocall
> +nanook
> +ncbi-blast+
> +ncbi-blast+-legacy,
> +ncbi-entrez-direct
> +ncbi-seg
> +ncl-tools
> +ncoils
> +neobio
> +nextsv
> +ngila
> +ngsqctoolkit
> +norsnet
> +norsp
> +nw-align
> +oases
> +obitools
> +obo-edit
> +octace-bioinfo
> +octave-bioinfo
> +oligoarrayaux
> +omegamap
> +operondb
> +pal2nal
>  paml
> -parallel
> -pass2
> -patch
> -perl
> -perl-doc
> -perl-modules
> -perl-tk
> +paraclu
> +parsinsert
> +parsnp
> +partigene
> +partitionfinder
> +patman
> +pbalign,
> +pbgenomicconsensus
> +pbsim
> +pcma
> +pdb2pqr
>  perm
> -pgadmin3
> -phylip
> -phyml
> +pfaat
> +pftools
> +phagefinder
> +phast
> +phipack
> +phybin
> +phylographer
> +phylophlan
> +phyloviz-core
> +physamp
> +phyutility
>  picard-tools
> -postgresql
> -postgresql-client
> +piler
> +pipasic,
> +plasmidomics
> +plato
> +plip
>  prank
> +predictnls
>  predictprotein
> +prime-phylo
>  primer3
> -probcons
> +probabel
> +prodigal
> +profbval
> +profisis
> +profit
> +profnet-bval,
> +profphd
> +profphd-net,
> +proftmb
> +progressivemauve
> +prokka
> +prot4est
> +proteinortho
> +pscan-tfbs
> +psipred
> +psortb
> +pssh2
> +pycorrfit
> +pyfai
>  pynast
> -python
> -python-all-dev
> -python-biopython
> -python-biopython-doc
> -python-biopython-sql
> -python-cogent
> -python-rpy
> -python-rpy2
> -python-rpy-doc
> -python-scipy
> +pyrophosphate-tools
> +pyscanfcs
> +python3-bd2k
> +python3-biopython
> +python3-biotools
> +python3-bx
> +python3-consensuscore2
> +python3-csb
> +python3-cutadapt
> +python3-dendropy
> +python3-ete3
> +python3-gfapy
> +python3-gffutils
> +python3-hyphy
> +python3-intervaltree-bio
> +python3-misopy
> +python3-pbconsensuscore
> +python3-pybedtools
> +python3-pyfaidx
> +python3-pyfasta
> +python3-pymummer
> +python3-pyvcf
> +python3-ruffus
> +python3-skbio
> +python-biom-format
> +python-cobra
> +python-corepywrap,
> +python-freecontact
> +python-htseq
> +python-kineticstools
> +python-mmtk
> +python-orange
> +python-pbcommand
> +python-pbcore,
> +python-pysam
> +python-rdkit
> +python-reaper
> +python-screed
> +python-treetime
> +qtlcart
> +qtltools
> +qualimap
> +raccoon
> +radiant
> +rambo-k
> +rapmap
>  rasmol
> +raster3d
> +rate4site
>  raxml
> -r-base
> -r-base-core
> -r-base-dev
> -r-base-html
> -r-bioc-affy
> -r-bioc-affyio
> -r-bioc-annotate
> -r-bioc-annotationdbi
> +ray
>  r-bioc-biobase
> -r-bioc-biocgenerics
> -r-bioc-biocinstaller
> -r-bioc-biomart
> -r-bioc-biostrings
> -r-bioc-bitseq
> -r-bioc-deseq
> -r-bioc-edger
> -r-bioc-genefilter
> -r-bioc-geneplotter
> -r-bioc-genomicranges
> +r-bioc-cummerbund
> +r-bioc-deseq2
> +r-bioc-deseq2,
> +r-bioc-ebseq
>  r-bioc-hilbertvis
> -r-bioc-impute
> -r-bioc-iranges
>  r-bioc-limma
> -r-bioc-multtest
> -r-bioc-pcamethods
> -r-bioc-preprocesscore
> -r-bioc-qvalue
> -r-bioc-rsamtools
> -r-bioc-zlibbioc
> -r-cran-abind
> -r-cran-ade4
> +r-bioc-mergeomics
> +r-bioc-metagenomeseq
> +r-bioc-metagenomeseq,
> +r-bioc-rtracklayer,
> +rbs-finder
> +r-cran-adegenet,
>  r-cran-ape
> -r-cran-aplpack
> -r-cran-bitops
> -r-cran-catools
> -r-cran-cluster
> -r-cran-dbi
> -r-cran-dichromat
> -r-cran-digest
> -r-cran-evaluate
> -r-cran-gdata
> -r-cran-gee
> -r-cran-getopt
> -r-cran-ggplot2
> -r-cran-gplots
> -r-cran-gtable
> -r-cran-gtools
> -r-cran-labeling
> -r-cran-lattice
> -r-cran-leaps
> -r-cran-lme4
> -r-cran-locfit
> -r-cran-matrix
> -r-cran-matrixstats
> -r-cran-munsell
> -r-cran-nlme
> -r-cran-optparse
> -r-cran-permute
> -r-cran-plotrix
> -r-cran-plyr
> -r-cran-prettyr
> -r-cran-proto
> -r-cran-rcolorbrewer
> -r-cran-rcpp
> -r-cran-rcurl
> -r-cran-relimp
> -r-cran-reshape2
> -r-cran-rggobi
> -r-cran-rgl
> -r-cran-rgtk2
> -r-cran-r.methodss3
> -r-cran-rmpi
> -r-cran-rserve
> -r-cran-rsqlite
> -r-cran-rwave
> -r-cran-samr
> -r-cran-scales
> -r-cran-scatterplot3d
> -r-cran-snow
> -r-cran-snowfall
> -r-cran-sp
> -r-cran-stringr
> -r-cran-tcltk2
> -r-cran-testthat
> +r-cran-distory
> +r-cran-genetics,
> +r-cran-metamix
> +r-cran-phangorn
> +r-cran-pscbs
> +r-cran-rncl,
> +r-cran-rotl
> +r-cran-seqinr
> +r-cran-treescape
>  r-cran-vegan
> -r-cran-waveslim
> -r-cran-wavethresh
> -r-cran-xml
> -r-cran-xtable
> -r-doc-html
> -r-doc-info
> -r-doc-pdf
> -readseq
> -rkhunter
> -r-mathlib
> -r-recommended
> -rsync
> -runurl
> -samtools
> -screen
> -seaview
> +rdp-alignment,
> +reapr
> +relion-bin+gui
> +repeatmasker
> +repeatmasker-recon
> +reprof
> +rmblast
> +rnahybrid
> +rna-star
> +roadtrips
> +roary
> +roche454ace2caf
> +roguenarok
> +rose
> +rosetta
> +r-other-apmswapp
> +r-other-hms-dbmi-spp
> +r-other-mott-happy.hbrem
> +rsat
> +rsem
> +ruby-bio
> +ruby-crb-blast
> +saint
> +samtools,
> +sap
> +scrm
> +seer
> +segemehl
>  seqan-apps
>  seqan-dev
> +seq-gen
> +seqsero
> +sequenceconverter.app
>  sift
> -software-properties-common
> -sputnik-mononucleotide
> -ssake
> -sshfs
> -stacks
> -subversion
> -sudo
> -synaptic
> -t-coffee
> -texi2html
> -texinfo
> -texlive-base
> -texlive-latex-base
> -texlive-latex-extra
> -texlive-latex-recommended
> -time
> +sim4db
> +sistr
> +situs
> +smithwaterman
> +snap
> +snpeff
> +solvate
> +spaced
> +sparta
> +spice
> +splitstree
> +squizz
> +ssaha
> +sspace
> +ssw-align
> +staden
> +staden-io-lib-utils
> +strap,
> +suitename
> +sumtrees
> +surankco
> +swarm
> +tacg
> +tantan
> +taverna
> +taxinspector
> +tetra
> +theseus
> +tigr-glimmer-mg
> +tn-seqexplorer
> +tnseq-transit
>  tophat
> -traceroute
> +topp,
> +toppred
> +trace2dbest
> +tracetuner
> +transdecoder
>  transtermhp
> -tree
> -tree-puzzle
> -treeviewx
> +treebuilder3d
> +tripal
>  trnascan-se
> -ubuntu-desktop*
> +tvc
> +twain
>  ugene
> -unity-scope-bio-linux
> -unzip
> -velvet
> -velvet-example
> -velvet-long
> -velvetoptimiser
> -vim
> -vim-gnome
> -weblogo
> -wget
> -wise
> -x2goclient
> -x2goserver
> -x2goserver-xsession
> -xclip
> -xmlstarlet
> -xz-utils
> -zlib1g-dev
> -zsh
> +unc-fish
> +uniprime
> +varmatch
> +varna
> +varscan
> +vcftools
> +vienna-rna
> +vmd
> +wigeon
> +x-tandem-pipeline
> +zalign
> +zodiac-zeden

> abyss
> acacia
> ampliconnoise
> apache2
> beam2
> bio-linux-ampliconnoise
> bio-linux-archaeopteryx
> bio-linux-artemis
> bio-linux-assembly-conversion-tools
> bio-linux-backups
> bio-linux-big-blast
> bio-linux-blast
> bio-linux-bldp-files
> bio-linux-blixem
> bio-linux-cap3
> bio-linux-catchall
> bio-linux-cd-hit
> bio-linux-clustal
> bio-linux-cytoscape
> bio-linux-dendroscope
> bio-linux-dotter
> bio-linux-dust
> bio-linux-emboss
> bio-linux-fasta
> bio-linux-fastdnaml
> bio-linux-fastqc
> bio-linux-fasttree
> bio-linux-gap2caf
> bio-linux-glimmer3
> bio-linux-happy:i386
> bio-linux-hmmer
> bio-linux-jmotu
> bio-linux-jprofilegrid
> bio-linux-keyring
> bio-linux-lucy
> bio-linux-mate-desktop
> bio-linux-mcl
> bio-linux-mesquite
> bio-linux-mira
> bio-linux-mira-3rd-party
> bio-linux-mothur
> bio-linux-mrbayes
> bio-linux-msatfinder
> bio-linux-mspcrunch
> bio-linux-mummer
> bio-linux-muscle
> bio-linux-mview
> bio-linux-ncbi-tools-x11
> bio-linux-njplot
> bio-linux-nrdb
> bio-linux-ocount
> bio-linux-oligoarray
> bio-linux-oligoarrayaux
> bio-linux-omegamap
> bio-linux-paml
> bio-linux-pfaat
> bio-linux-phylip
> bio-linux-phyml
> bio-linux-priam
> bio-linux-primer3
> bio-linux-qiime
> bio-linux-qtlcart
> bio-linux-rasmol
> bio-linux-rbs-finder
> bio-linux-rdp-classifier
> bio-linux-readseq
> bio-linux-sampledata
> bio-linux-samtools
> bio-linux-splitstree
> bio-linux-squint
> bio-linux-staden
> bio-linux-stars
> bio-linux-tablet
> bio-linux-taxinspector
> bio-linux-t-coffee
> bio-linux-tetra
> bio-linux-themes-v8
> bio-linux-tree-puzzle
> bio-linux-treeview
> bio-linux-tutorials
> bio-linux-usb-maker
> bio-linux-xcut
> bio-linux-zsh
> bioperl
> bioperl-run
> biosquid
> blimps-utils
> bowtie
> bowtie2
> bowtie2-examples
> bowtie-examples
> bwa
> cdbfasta
> chimeraslayer
> chkrootkit
> cifs-utils
> cmake
> cufflinks
> curl
> cython
> cython-dbg
> debconf
> default-jdk
> dialign
> dictionaries-common
> eclipse
> emacs
> emacsen-common
> emacs-goodies-el
> estscan2
> evince
> evolution
> evolution-indicator
> fastdnaml
> fastjar
> fastx-toolkit
> g++
> galaxy-server-all
> gcc
> gedit
> gfortran
> gimp
> glam2
> gnome-session-fallback*
> gnuplot
> graphicsmagick
> graphviz
> hmmer
> hyphy
> icedtea-7-plugin
> indicator-applet-complete
> jalview
> jellyfish
> jemboss
> last-align
> lastz
> less
> libapache2-reload-perl
> libapache-dbi-perl
> libbiojava-java
> libbiojava-java-demos
> libc6-dev
> libconfig-simple-perl
> libdata-stag-perl
> libdbd-pg-perl
> libio-string-perl
> libmailtools-perl
> libspreadsheet-parseexcel-perl
> libspreadsheet-writeexcel-perl
> libtext-csv-perl
> lynx
> mafft
> make
> maq
> mcl
> mdadm
> meld
> meme
> meme-examples
> microbiomeutil
> mira-3rdparty
> mira-assembler
> mira-doc
> mira-examples
> mothur
> mrbayes
> mummer
> muscle
> mysql-client
> ncbi-tools-bin
> njplot
> openjdk-7-jdk
> openjdk-7-jre
> openmpi-bin
> openmpi-common
> openssh-server
> oswitch
> paml
> parallel
> pass2
> patch
> perl
> perl-doc
> perl-modules
> perl-tk
> perm
> pgadmin3
> phylip
> phyml
> picard-tools
> postgresql
> postgresql-client
> prank
> predictprotein
> primer3
> probcons
> pynast
> python
> python-all-dev
> python-biopython
> python-biopython-doc
> python-biopython-sql
> python-cogent
> python-rpy
> python-rpy2
> python-rpy-doc
> python-scipy
> rasmol
> raxml
> r-base
> r-base-core
> r-base-dev
> r-base-html
> r-bioc-affy
> r-bioc-affyio
> r-bioc-annotate
> r-bioc-annotationdbi
> r-bioc-biobase
> r-bioc-biocgenerics
> r-bioc-biocinstaller
> r-bioc-biomart
> r-bioc-biostrings
> r-bioc-bitseq
> r-bioc-deseq
> r-bioc-edger
> r-bioc-genefilter
> r-bioc-geneplotter
> r-bioc-genomicranges
> r-bioc-hilbertvis
> r-bioc-impute
> r-bioc-iranges
> r-bioc-limma
> r-bioc-multtest
> r-bioc-pcamethods
> r-bioc-preprocesscore
> r-bioc-qvalue
> r-bioc-rsamtools
> r-bioc-zlibbioc
> r-cran-abind
> r-cran-ade4
> r-cran-ape
> r-cran-aplpack
> r-cran-bitops
> r-cran-catools
> r-cran-cluster
> r-cran-dbi
> r-cran-dichromat
> r-cran-digest
> r-cran-evaluate
> r-cran-gdata
> r-cran-gee
> r-cran-getopt
> r-cran-ggplot2
> r-cran-gplots
> r-cran-gtable
> r-cran-gtools
> r-cran-labeling
> r-cran-lattice
> r-cran-leaps
> r-cran-lme4
> r-cran-locfit
> r-cran-matrix
> r-cran-matrixstats
> r-cran-munsell
> r-cran-nlme
> r-cran-optparse
> r-cran-permute
> r-cran-plotrix
> r-cran-plyr
> r-cran-prettyr
> r-cran-proto
> r-cran-rcolorbrewer
> r-cran-rcpp
> r-cran-rcurl
> r-cran-relimp
> r-cran-reshape2
> r-cran-rggobi
> r-cran-rgl
> r-cran-rgtk2
> r-cran-r.methodss3
> r-cran-rmpi
> r-cran-rserve
> r-cran-rsqlite
> r-cran-rwave
> r-cran-samr
> r-cran-scales
> r-cran-scatterplot3d
> r-cran-snow
> r-cran-snowfall
> r-cran-sp
> r-cran-stringr
> r-cran-tcltk2
> r-cran-testthat
> r-cran-vegan
> r-cran-waveslim
> r-cran-wavethresh
> r-cran-xml
> r-cran-xtable
> r-doc-html
> r-doc-info
> r-doc-pdf
> readseq
> rkhunter
> r-mathlib
> r-recommended
> rsync
> runurl
> samtools
> screen
> seaview
> seqan-apps
> seqan-dev
> sift
> software-properties-common
> sputnik-mononucleotide
> ssake
> sshfs
> stacks
> subversion
> sudo
> synaptic
> t-coffee
> texi2html
> texinfo
> texlive-base
> texlive-latex-base
> texlive-latex-extra
> texlive-latex-recommended
> time
> tophat
> traceroute
> transtermhp
> tree
> tree-puzzle
> treeviewx
> trnascan-se
> ubuntu-desktop*
> ugene
> unity-scope-bio-linux
> unzip
> velvet
> velvet-example
> velvet-long
> velvetoptimiser
> vim
> vim-gnome
> weblogo
> wget
> wise
> x2goclient
> x2goserver
> x2goserver-xsession
> xclip
> xmlstarlet
> xz-utils
> zlib1g-dev
> zsh

> 
> abacas
> abyss
> acacia
> acedb-other
> adapterremoval
> adun-core
> aegean
> aevol
> alien-hunter
> alter-sequence-alignment
> amap-align
> amos-assembler,
> amoscmp
> ampliconnoise
> andi
> apollo
> arachne
> aragorn
> arb
> ariba
> artemis
> asap
> atac
> augustus
> autodock
> autodocktools,
> autodock-vina
> autogrid
> avogadro,
> axe-demultiplexer
> axparafit,
> bagpipe
> baitfisher
> ballview
> bambus
> bandage
> barrnap
> beads
> beagle
> beast-mcmc
> beast-mcmc,
> bedops
> biceps
> big-blast
> bigsdb
> bioclipse
> bio-eagle
> bioperl,
> biosquid
> bitseq
> blasr
> blat
> blimps-utils
> blixem,
> blobology
> bowtie,
> boxshade,
> bppsuite,
> btk-core
> bwa
> cactus
> caftools
> card-rgi
> cassiopee
> ccs
> cdbfasta
> cd-hit
> cdna-db
> cellprofiler
> centrifuge
> cgview,
> cinema
> circlator
> circos,
> clearcut
> clonalframe,
> clonalorigin
> clustalx
> clustalx,
> cluster3
> cmap
> cnvkit
> codonw
> compclust
> concavity
> condetri
> conservation-code
> contrafold
> contralign
> coot
> copycat
> crossbow
> crux-toolkit
> csb
> cytoscape
> daligner
> das-proserver
> dawg
> dazzdb
> dazzle
> decipher
> diamond-aligner
> discosnp
> discosnp,
> disulfinder
> dssp
> ecell
> ecopcr
> edtsurf
> e-hive
> eigensoft
> elph
> embassy-domalign,
> emboss
> emmax
> emperor
> ensembl
> est-db
> estferret
> estscan
> euler2,
> exabayes
> exalt
> examl,
> excavator
> falcon
> fasta
> fasta3
> fastahack
> fastlink,
> fastml
> fastqtl
> fasttree
> fastx-toolkit
> ffindex
> ffp
> figaro
> finex
> fitgcp
> freebayes
> freecontact
> fsa
> galaxy
> garli
> gasic
> gassst
> gatb-core
> gatk
> gbrowse
> gbrowse-syn
> genemark
> genesplicer
> genetrack
> genezilla
> genographer
> genometools
> gentle
> gff2ps,
> glam2
> glimmerhmm
> gmv
> grabix
> graphlan
> gromacs
> gubbins
> gwama
> haploview
> harvest-tools
> hexamer
> hhsuite
> hilbertvisgui
> hmmer2
> htqc
> hyphygui,
> indelible
> infernal
> ipig
> jaligner
> jalview
> jbrowse
> jellyfish
> jigsaw
> kempbasu
> kineticstools
> king-probe
> kmc
> kmer
> lagan
> lamarc
> lambda-align
> leaff
> lefse
> libace-perl
> libai-fann-perl
> libbambamc-dev
> libbamtools-dev
> libbiococoa-dev
> libbio-das-lite-perl
> libbiod-dev
> libbio-eutilities-perl
> libbio-graphics-perl,
> libbiojava-java,
> libbio-mage-perl
> libbio-mage-utils-perl
> libbio-primerdesigner-perl
> libbpp-core-dev,
> libchado-perl
> libdivsufsort-dev
> libfast5-dev,
> libfastahack-dev
> libffindex0-dev
> libfml-dev
> libforester-java
> libfreecontact-dev,
> libgatbcore-dev
> libgenome-1.3-dev,
> libgenome-perl,
> libgenometools0-dev
> libgff-dev
> libgff-perl
> libgkarrays-dev
> libgoby-java
> libgo-perl
> libhmsbeagle-dev
> libhts-dev
> libhtsjdk-java
> libjebl2-java
> libjloda-java
> libkmer-dev
> libminimap-dev
> libncl-dev
> libngs-sdk-dev,
> libnhgri-blastall-perl
> libopenms-dev
> libpal-java
> libpbbam-dev
> libpbseq-dev,
> libqcpp-dev
> libqes-dev
> librdp-taxonomy-tree-java
> librelion-dev
> librg-blast-parser-perl
> librg-reprof-bundle-perl
> librg-utils-perl
> libroadrunner-dev,
> librostlab3-dev
> librostlab-blast0-dev
> libsbml5-dev,
> libseqlib-dev
> libsmithwaterman-dev
> libsnp-sites1-dev
> libsort-key-top-perl
> libsrf-dev
> libssm-dev
> libssw-dev,
> libstaden-read-dev
> libswiss-perl
> libtabixpp-dev
> libtfbs-perl
> libvcflib-dev
> libvibrant6-dev
> libzerg0-dev,
> lofreq
> logol-bin
> ltrsift
> lucy
> mach-haplotyper
> macsyfinder
> maffilter
> mafft
> mage2tab,
> maker2
> malt
> manta
> mapsembler2
> martj
> mash
> mauve-aligner
> maxd
> mcl
> melting
> meme
> meryl
> mesquite
> metabit
> metaphlan2
> metarep
> metastudent
> mgltools-networkeditor,
> mhap
> microbegps
> microbiomeutil
> microbiomeutil,
> migrate
> minia
> miniasm
> minimap
> minimus
> mipe
> mirbase
> mlv-smile
> modeller
> molekel
> mothur
> mothur,
> mpsqed
> mptp
> msatfinder
> mugsy
> mummer,
> mummergpu
> murasaki
> muscle
> mview
> nanocall
> nanook
> ncbi-blast+
> ncbi-blast+-legacy,
> ncbi-entrez-direct
> ncbi-seg
> ncl-tools
> ncoils
> neobio
> nextsv
> ngila
> ngsqctoolkit
> norsnet
> norsp
> nw-align
> oases
> obitools
> obo-edit
> octace-bioinfo
> octave-bioinfo
> oligoarrayaux
> omegamap
> operondb
> pal2nal
> paml
> paraclu
> parsinsert
> parsnp
> partigene
> partitionfinder
> patman
> pbalign,
> pbgenomicconsensus
> pbsim
> pcma
> pdb2pqr
> perm
> pfaat
> pftools
> phagefinder
> phast
> phipack
> phybin
> phylographer
> phylophlan
> phyloviz-core
> physamp
> phyutility
> picard-tools
> piler
> pipasic,
> plasmidomics
> plato
> plip
> prank
> predictnls
> predictprotein
> prime-phylo
> primer3
> probabel
> prodigal
> profbval
> profisis
> profit
> profnet-bval,
> profphd
> profphd-net,
> proftmb
> progressivemauve
> prokka
> prot4est
> proteinortho
> pscan-tfbs
> psipred
> psortb
> pssh2
> pycorrfit
> pyfai
> pynast
> pyrophosphate-tools
> pyscanfcs
> python3-bd2k
> python3-biopython
> python3-biotools
> python3-bx
> python3-consensuscore2
> python3-csb
> python3-cutadapt
> python3-dendropy
> python3-ete3
> python3-gfapy
> python3-gffutils
> python3-hyphy
> python3-intervaltree-bio
> python3-misopy
> python3-pbconsensuscore
> python3-pybedtools
> python3-pyfaidx
> python3-pyfasta
> python3-pymummer
> python3-pyvcf
> python3-ruffus
> python3-skbio
> python-biom-format
> python-cobra
> python-corepywrap,
> python-freecontact
> python-htseq
> python-kineticstools
> python-mmtk
> python-orange
> python-pbcommand
> python-pbcore,
> python-pysam
> python-rdkit
> python-reaper
> python-screed
> python-treetime
> qtlcart
> qtltools
> qualimap
> raccoon
> radiant
> rambo-k
> rapmap
> rasmol
> raster3d
> rate4site
> raxml
> ray
> r-bioc-biobase
> r-bioc-cummerbund
> r-bioc-deseq2
> r-bioc-deseq2,
> r-bioc-ebseq
> r-bioc-hilbertvis
> r-bioc-limma
> r-bioc-mergeomics
> r-bioc-metagenomeseq
> r-bioc-metagenomeseq,
> r-bioc-rtracklayer,
> rbs-finder
> r-cran-adegenet,
> r-cran-ape
> r-cran-distory
> r-cran-genetics,
> r-cran-metamix
> r-cran-phangorn
> r-cran-pscbs
> r-cran-rncl,
> r-cran-rotl
> r-cran-seqinr
> r-cran-treescape
> r-cran-vegan
> rdp-alignment,
> reapr
> relion-bin+gui
> repeatmasker
> repeatmasker-recon
> reprof
> rmblast
> rnahybrid
> rna-star
> roadtrips
> roary
> roche454ace2caf
> roguenarok
> rose
> rosetta
> r-other-apmswapp
> r-other-hms-dbmi-spp
> r-other-mott-happy.hbrem
> rsat
> rsem
> ruby-bio
> ruby-crb-blast
> saint
> samtools,
> sap
> scrm
> seer
> segemehl
> seqan-apps
> seqan-dev
> seq-gen
> seqsero
> sequenceconverter.app
> sift
> sim4db
> sistr
> situs
> smithwaterman
> snap
> snpeff
> solvate
> spaced
> sparta
> spice
> splitstree
> squizz
> ssaha
> sspace
> ssw-align
> staden
> staden-io-lib-utils
> strap,
> suitename
> sumtrees
> surankco
> swarm
> tacg
> tantan
> taverna
> taxinspector
> tetra
> theseus
> tigr-glimmer-mg
> tn-seqexplorer
> tnseq-transit
> tophat
> topp,
> toppred
> trace2dbest
> tracetuner
> transdecoder
> transtermhp
> treebuilder3d
> tripal
> trnascan-se
> tvc
> twain
> ugene
> unc-fish
> uniprime
> varmatch
> varna
> varscan
> vcftools
> vienna-rna
> vmd
> wigeon
> x-tandem-pipeline
> zalign
> zodiac-zeden



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