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/

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

comrna:     http://stormo.wustl.edu/comRNA/

contrafold: http://contra.stanford.edu/contrafold/
	    http://bioinformatics.oxfordjournals.org/content/22/14/e90.abstract

covea:      ???

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.

foldalign:  http://foldalign.ku.dk/software/

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

rdp-classifier: Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rdp-classifier/trunk/
            Packaging prepared, preconditions in new queue

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
