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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
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