--- Begin Message ---
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:'.
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:tony.travis@minke-informatics.co.uk
--- 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
--- End Message ---