PyCogent for Debian
-------------------

Note that not all unit tests are working.  At package build time only
those tests are ran that do not fail.  The test results are reflected
in the package dependencies:  If a test runs the tested tool is listed
as Recommends - otherwise the tool is only Suggested (since not tested).

There is some work left to fix the tests for all tools.  It is suspected
that the tools just evolved and changed their interface.  Volunteers to
adapt the tests are welcome.


The following external tools are supported by PyCogent but not yet
packaged for Debian:


blat:       http://anonscm.debian.org/gitweb/?p=debian-med/blat.git
            Packaging prepared but licensing issues

carnac:     http://bioinfo.lifl.fr/carnac/
            Asket upstream about versioned tarball

cmfinder:   http://bio.cs.washington.edu/yzizhen/CMfinder/
            registration page

comrna:     http://stormo.wustl.edu/comRNA/
            needs contact about license: If you are a commercial user or want to commercialize it, please contact the authors.

contrafold: http://contra.stanford.edu/contrafold/
	    http://bioinformatics.oxfordjournals.org/content/22/14/e90.abstract
            Packaging prepared at https://anonscm.debian.org/git/debian-med/contrafold.git

covea:      not sure - may be part of (non-free) trnascan-se
            https://anonscm.debian.org/git/debian-med/trnascan-se.git

dynalign:   http://rna.urmc.rochester.edu/dynalign.html
            Mathews DH, Turner DH (2002). "Dynalign: an algorithm for finding the secondary structure common to two RNA sequences". J. Mol. Biol. 317 (2): 191–203. doi:10.1006/jmbi.2001.5351. PMID 11902836.
            Note that Dynalign is now fully incorporated into the RNAstructure package
              -->  http://rna.urmc.rochester.edu/RNAstructure.html<->(GPL, but registration)

foldalign:  http://rth.dk/resources/foldalign/
            http://bioinformaticsreview.com/20160413/foldalign-a-tool-for-secondary-structure-alignment-of-rna/
             == https://www.ncbi.nlm.nih.gov/pubmed/26704597

guppy:      https://staff.aist.go.jp/yutaka.ueno/guppy/

ilm:        ???

knetfold:   http://knetfold.abcc.ncifcrf.gov/

mfold:      http://mfold.rna.albany.edu/?q=mfold/download-mfold

msms:       ???

pplacer:    http://www.mybiosoftware.com/phylogenetic-analysis/5069

Fold.out    ???

PETfold:    http://rth.dk/resources/petfold/download.html
            (findphyl)

pknotsRG:   http://www.hsls.pitt.edu/obrc/index.php?page=URL1212590768

rnaview:    http://www.mybiosoftware.com/rna-analysis/1141