Hi, Andreas. Re: Our discussion at the 2018 Debian-Med Sprint in Barcelona.
I've compared our Bio-Linux 'master' package list used to create the 'live/install' USB stick with your "med-bio*" list of 'Recommends:'. Updated to remove ',' from the end of "med-bio*" package names and the "bio-linux-" prefix from the Bio-Linux 'master' package list. Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:[email protected]
--- bl_package_list.txt 2018-02-11 19:10:52.727650855 +0100 +++ debian-med-bio.list 2018-02-11 19:13:54.551645483 +0100 @@ -1,319 +1,544 @@ +abacas abyss acacia -apache2 -archaeopteryx +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 -assembly-conversion-tools -backups -beam2 +asap +atac +augustus +autodock +autodocktools +autodock-vina +autogrid +avogadro +axe-demultiplexer +axparafit +bagpipe +baitfisher +ballview +bambus +bandage +barrnap +beads +beagle +bedops +biceps big-blast +bigsdb +bioclipse +bio-eagle bioperl -bioperl-run biosquid -blast -bldp-files +bitseq +blasr +blat blimps-utils blixem +blobology bowtie -bowtie2 -bowtie2-examples -bowtie-examples +boxshade +bppsuite +btk-core bwa -cap3 -catchall +cactus +caftools +card-rgi +cassiopee +ccs cdbfasta cd-hit -chimeraslayer -chkrootkit -cifs-utils -clustal -cmake -cufflinks -curl -cython -cython-dbg +cdna-db +cellprofiler +centrifuge +cgview +cinema +circlator +circos +clearcut +clonalframe +clonalorigin +cluster3 +cmap +cnvkit +codonw +compclust +concavity +condetri +conservation-code +contrafold +contralign +coot +copycat +crossbow +crux-toolkit +csb cytoscape -debconf -default-jdk -dendroscope -dialign -dictionaries-common -dotter -dust -eclipse -emacs -emacsen-common -emacs-goodies-el +daligner +das-proserver +dawg +dazzdb +dazzle +decipher +diamond-aligner +disulfinder +dssp +ecell +ecopcr +edtsurf +e-hive +eigensoft +elph +embassy-domalign emboss -estscan2 -evince -evolution -evolution-indicator +emmax +emperor +ensembl +est-db +estferret +estscan +euler2 +exabayes +exalt +examl +excavator +falcon fasta -fastjar -fastqc +fasta3 +fastahack +fastlink +fastml +fastqtl fasttree fastx-toolkit -g++ -galaxy-server-all -gap2caf -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 -glimmer3 -gnome-session-fallback* -gnuplot -graphicsmagick -graphviz -happy:i386 -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 -jmotu -jprofilegrid -keyring -last-align -lastz -less -libapache2-reload-perl -libapache-dbi-perl +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 -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 +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 -lynx +mach-haplotyper +macsyfinder +maffilter mafft -make -maq -mate-desktop -mdadm -meld +mage2tab +maker2 +malt +manta +mapsembler2 +martj +mash +mauve-aligner +maxd +mcl +melting meme -meme-examples +meryl mesquite -microbiomeutil -mira -mira-3rdparty -mira-3rd-party -mira-assembler -mira-doc -mira-examples +metabit +metaphlan2 +metarep +metastudent +mgltools-networkeditor +mhap +microbegps +migrate +minia +miniasm +minimap +minimus +mipe +mirbase +mlv-smile +modeller +molekel +mpsqed +mptp msatfinder -mspcrunch +mugsy +mummer +mummergpu +murasaki +muscle mview -mysql-client -ncbi-tools-bin -ncbi-tools-x11 -nrdb -ocount -oligoarray +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 -openjdk-7-jdk -openjdk-7-jre -openmpi-bin -openmpi-common -openssh-server -oswitch -parallel -pass2 -patch -perl -perl-doc -perl-modules -perl-tk +operondb +pal2nal +paml +paraclu +parsinsert +parsnp +partigene +partitionfinder +patman +pbalign +pbgenomicconsensus +pbsim +pcma +pdb2pqr perm pfaat -pgadmin3 +pftools +phagefinder +phast +phipack +phybin +phylographer +phylophlan +phyloviz-core +physamp +phyutility picard-tools -postgresql -postgresql-client +piler +pipasic +plasmidomics +plato +plip prank +predictnls predictprotein -priam -probcons +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 -python -python-all-dev -python-biopython -python-biopython-doc -python-biopython-sql -python-cogent -python-rpy -python-rpy2 -python-rpy-doc -python-scipy -qiime +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-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-bioc-mergeomics +r-bioc-rtracklayer rbs-finder -r-cran-abind -r-cran-ade4 +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 -rdp-classifier -rkhunter -r-mathlib -r-recommended -rsync -runurl -sampledata -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 +sim4db +sistr +situs +smithwaterman +snap +snpeff +solvate +spaced +sparta +spice splitstree -sputnik-mononucleotide -squint -ssake -sshfs -stacks +squizz +ssaha +sspace +ssw-align staden -stars -subversion -sudo -synaptic -tablet +staden-io-lib-utils +strap +suitename +sumtrees +surankco +swarm +tacg +tantan +taverna taxinspector tetra -texi2html -texinfo -texlive-base -texlive-latex-base -texlive-latex-extra -texlive-latex-recommended -themes-v8 -time +theseus +tigr-glimmer-mg +tn-seqexplorer +tnseq-transit tophat -traceroute +topp +toppred +trace2dbest +tracetuner +transdecoder transtermhp -tree -treeview -treeviewx +treebuilder3d +tripal trnascan-se -tutorials -ubuntu-desktop* +tvc +twain ugene -unity-scope-bio-linux -unzip -usb-maker -velvet -velvet-example -velvet-long -velvetoptimiser -vim -vim-gnome -weblogo -wget -wise -x2goclient -x2goserver -x2goserver-xsession -xclip -xcut -xmlstarlet -xz-utils -zlib1g-dev +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
abyss acacia apache2 archaeopteryx artemis assembly-conversion-tools backups beam2 big-blast bioperl bioperl-run biosquid blast bldp-files blimps-utils blixem bowtie bowtie2 bowtie2-examples bowtie-examples bwa cap3 catchall cdbfasta cd-hit chimeraslayer chkrootkit cifs-utils clustal cmake cufflinks curl cython cython-dbg cytoscape debconf default-jdk dendroscope dialign dictionaries-common dotter dust eclipse emacs emacsen-common emacs-goodies-el emboss estscan2 evince evolution evolution-indicator fasta fastjar fastqc fasttree fastx-toolkit g++ galaxy-server-all gap2caf gcc gedit gfortran gimp glam2 glimmer3 gnome-session-fallback* gnuplot graphicsmagick graphviz happy:i386 hyphy icedtea-7-plugin indicator-applet-complete jalview jellyfish jemboss jmotu jprofilegrid keyring 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 lucy lynx mafft make maq mate-desktop mdadm meld meme meme-examples mesquite microbiomeutil mira mira-3rdparty mira-3rd-party mira-assembler mira-doc mira-examples msatfinder mspcrunch mview mysql-client ncbi-tools-bin ncbi-tools-x11 nrdb ocount oligoarray oligoarrayaux omegamap openjdk-7-jdk openjdk-7-jre openmpi-bin openmpi-common openssh-server oswitch parallel pass2 patch perl perl-doc perl-modules perl-tk perm pfaat pgadmin3 picard-tools postgresql postgresql-client prank predictprotein priam 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 qiime qtlcart 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 rbs-finder 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 rdp-classifier rkhunter r-mathlib r-recommended rsync runurl sampledata screen seaview seqan-apps seqan-dev sift software-properties-common splitstree sputnik-mononucleotide squint ssake sshfs stacks staden stars subversion sudo synaptic tablet taxinspector tetra texi2html texinfo texlive-base texlive-latex-base texlive-latex-extra texlive-latex-recommended themes-v8 time tophat traceroute transtermhp tree treeview treeviewx trnascan-se tutorials ubuntu-desktop* ugene unity-scope-bio-linux unzip usb-maker velvet velvet-example velvet-long velvetoptimiser vim vim-gnome weblogo wget wise x2goclient x2goserver x2goserver-xsession xclip xcut xmlstarlet xz-utils zlib1g-dev
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 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 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 disulfinder dssp ecell ecopcr edtsurf e-hive eigensoft elph embassy-domalign emboss emmax emperor ensembl est-db 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minia miniasm minimap minimus mipe mirbase mlv-smile modeller molekel 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-ebseq r-bioc-hilbertvis r-bioc-limma r-bioc-mergeomics 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
