I finally removed what **I** think is in Debian - may be somebody does a double check

    at  http://sites.stat.psu.edu/~yzz2/software/

  - This article https://academic.oup.com/bioinformatics/article/26/20/2517/194775

    might be related

bioperl-run:

  - ??? This is in Debian

blast:

  - ??? This is in Debian - may be blast2 or ncbi-blast+-legacy ?

bldp-files

bowtie2, bowtie2-examples, bowtie-examples:

  - ??? This is in Debian

cap3:

  - http://seq.cs.iastate.edu/cap3.html

  - also used in ugene

  - link to source bounces, ask authors

  - https://www.ncbi.nlm.nih.gov/pubmed/21121040,

   https://www.ncbi.nlm.nih.gov/pubmed/22333246

chimeraslayer:

  - ??? This is in Debian (inside microbiomeutil source package)

clustal:

  - ??? do you mean clustalo, clustalw or clustalx

cufflinks:

  - ??? This is in non-free (thus available as package)

dendroscope:

  - https://github.com/danielhuson/dendroscope3

  - http://dendroscope.org/

  - Should be packaged since used by beast2

  - Asked for Release tags: https://github.com/danielhuson/dendroscope3/issues/8

dialign:

  - ??? Debian has dialign and dialign-tx

dotter

  - ??? Just packaged and is available, will be included in next med-bio metapackage

dust:

  - https://github.com/lh3/mdust

    mdust from DFCI Gene Indices Software Tools (archived for a historical record only)

emmax:

  - https://anonscm.debian.org/git/debian-med/emmax.git

  - Asked author for license

fastqc:

  - ??? Available in Debian

galaxy-server-all:

  - https://galaxyproject.org/

gap2caf:

  - http://www.sanger.ac.uk/science/tools/caf

glimmer3

  - ??? Avaliable as tigr-glimmer

happy:

  - ??? do you mean r-other-mott-happy which is in Debian?

hyphy:

  - ??? Available as hyphy-mpi

jemboss:

  - ??? in Debian

jmotu:

  - http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019259

  - It is refering to http://www.nematodes.org/ which seems to be offline but

jprofilegrid:

  - http://www.profilegrid.org/

  - Download available, claims to be GPL

last-align:

  - ??? Availanle in Debian

lastz:

  - https://github.com/lastz/lastz

    (might be an easy target)

libbiojava-java-demos

  - ??? Debian has libbiojava - what files should be provided as demos

-libio-string-perl

maq:

  - ??? Available in Debian

meme, meme-examples:

  - https://anonscm.debian.org/git/debian-med/meme.git

  - Package in non-free, needs to be finalised

  - Ask authors for free license

microbiomeutil:

  - ??? in Debian

mira, mira-3rdparty, mira-3rd-party, mira-doc, mira-examples

  - What is the difference between mira and mira-assembler

mira-assembler

  - ??? in Debian

mspcrunch:

  - http://sonnhammer.org/MSPcrunch.html

  - Source at http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/

ncbi-tools-bin, ncbi-tools-x11:

  - ??? both are in Debian

nrdb:

  - Situation unclear.  According to http://seqanswers.com/forums/showthread.php?t=6697

    Seems you can some ask for some private license.  Moreover

    No idea how we can obtain the source from there

priam:

  - http://priam.prabi.fr/

probcons:

  - ??? in Debian

qiime:

  - Debian has an old version of qiime but the new version

    is not installable due to non-buildable python-burrito-fillings

r-bioc-affy:

r-bioc-affyio:

r-bioc-annotate:

r-bioc-annotationdbi:

r-bioc-biocgenerics:

r-bioc-biocinstaller:

r-bioc-biomart:

r-bioc-biostrings:

r-bioc-genefilter:

r-bioc-geneplotter:

r-bioc-genomicranges:

r-bioc-impute:

r-bioc-iranges:

r-bioc-limma:

r-bioc-multtest:

r-bioc-preprocesscore:

r-bioc-qvalue:

r-bioc-rsamtools:

  - All these are available in Debian but not explicitly specified

    in med-bio task since these are implicitly installed due to

    dependencies

r-bioc-zlibbioc:

  - That's not needed - Debian uses plain zlib

-r-bioc-edger:

  - Used to be in Debian in an old version.  edger now depends from

    locfit which is non-distributable

  - All missing R packages in new queue

r-cran-locfit:

  - can not be packaged due to license issues -> http://bugs.debian.org/731599

r-cran-abind:

r-cran-ade4:

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-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-scales:

r-cran-scatterplot3d:

r-cran-snow:

r-cran-sp:

r-cran-stringr:

r-cran-tcltk2:

r-cran-testthat:

r-cran-xml:

r-cran-xtable:

r-doc-html:

r-doc-info:

r-doc-pdf:

r-mathlib:

r-recommended:

  - All these are available in Debian but not explicitly specified

    in med-bio task since these are implicitly installed due to

    dependencies

rdp-classifier:

  - ??? in Debian

runurl:

  - Please explain - are you refering to https://shiny.rstudio.com/reference/shiny/0.11/runUrl.html ?

sampledata:

  - Sounds pretty BioLinux specific.  Let us know if we should include something into Debian.

seaview:

  - ??? in Debian

sputnik-mononucleotide

  - https://bitbucket.org/natefoo/sputnik-mononucleotide

squint:

  - http://www.bioinformatics.org.nz/en/about/tools-and-resources/software-tools/squint.html

  - https://www.ncbi.nlm.nih.gov/pubmed/17485434

ssake:

  - ??? in Debian

stacks:

  - ??? in Debian

stars:

  - https://sourceforge.net/projects/stars/

    Latest version of 2004 accessing very old staden version - is this of any use?

  - https://ics.hutton.ac.uk/tablet/

themes-v8:

  - BioLinux specific but it could be packaged in principle

treeview:

treeviewx:

  - ??? both are in Debian

tutorials:

  - BioLinux specific but it could be packaged in principle

velvet:

velvet-example:

velvet-long:

velvetoptimiser:

  - ??? all in Debian

weblogo:

  - http://weblogo.threeplusone.com/

wise:

  - ??? in Debian