[Blends-commit] r3122 - /projects/debug/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Thu Jan 26 21:55:46 2012
New Revision: 3122

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3122
Log:
Need to debug bio task

Added:
    projects/debug/tasks/bio

Added: projects/debug/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/debug/tasks/bio?rev=3122&op=file
==============================================================================
--- projects/debug/tasks/bio (added)
+++ projects/debug/tasks/bio Thu Jan 26 21:55:46 2012
@@ -1,0 +1,3947 @@
+Task: Biology
+Description: Debian Med micro-biology packages
+ This metapackage will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences.
+
+X-Begin-Category: Phylogenetic analysis
+
+Depends: altree
+Remark: altree 1.1.0 should be not be packaged
+ According to Vincent Danjean <vdanjean.ml at free.fr> version 1.1.0 should not
+ be packaged for two reasons:
+ .
+  1. New dependencies (libtamuanova-perl, nanova and libnanova-perl) which
+     need to be packaged.
+  2. There are still bugs in the new method added in altree 1.1.0 and the doc
+     is not updated.
+ .
+ See http://lists.debian.org/debian-med/2009/08/msg00104.html for further
+ details.
+
+Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
+
+Depends: probalign
+
+Depends: treeviewx
+X-Published-Authors: FIXME
+X-Published-Title: FIXME
+Published-In: Computer Applications in the Bioscience 12:357-358
+Published-Year: 1996
+
+Depends: figtree
+
+X-End-Category: Phylogenetic analysis
+
+Depends:     molphy, phylip
+Why:         Phylogenetic analysis (Non-free, thus only suggested).
+
+X-Comment: treetool is removed from Debian because it is not maintained upstream since
+ 1995 and cause the Xserver to freeze under Squeeze
+
+Depends:     fastlink, loki, plink, r-cran-qtl
+Why:         Genetics
+
+X-Begin-Category: Sequence alignments and related programs.
+
+Depends:     amap-align
+Remark: Dead upstream
+ The homepage of this project vanished as well as the Download area.  An
+ old unmaintained version remained at code.google.com.  Please drop the
+ maintainer a note if you have any news of this project.
+
+Depends:     boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+
+Depends:     maqview
+
+Depends: bwa
+Published-Title: Fast and accurate short read alignment with Burrows-Wheeler transform
+Published-Authors: Li, Heng and Durbin, Richard
+Published-In: Bioinformatics 25(14):1754-1760
+Published-Year: 2009
+Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754
+
+Depends: mummer
+Published-Title: Versatile and open software for comparing large genomes
+Published-Authors: Stefan Kurtz, Adam Phillippy, Arthur L. Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L. Salzberg
+Published-In: Genome Biol. 5(2):R12
+Published-Year: 2004
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/14759262
+Published-DOI: 10.1186/gb-2004-5-2-r12
+Published-PubMed: 14759262
+
+Depends: blast2
+Published-Title: Basic local alignment search tool
+Published-Authors: S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman
+Published-In: J Mol Biol. 215(3):403-410
+Published-Year: 1990
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/2231712
+
+Depends: mafft
+Published-Title: Multiple alignment of DNA sequences with MAFFT
+Published-Authors: K. Katoh, G. Asimenos, H. Toh
+Published-In: Methods Mol Biol. 537:39-64
+Published-Year: 2009
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19378139
+Published-PubMed: 19378139
+
+Depends: t-coffee
+Published-Title: T-Coffee: A novel method for multiple sequence alignments
+Published-Authors: C. Notredame, D. Higgins, J. Heringa
+Published-In: Journal of Molecular Biology 302(1):205-217
+Published-Year: 2000
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
+Published-PubMed: 10964570
+Remark: Do not update to version 9.0
+ Version 9.0 contains non-free code.  See http://bugs.debian.org/649263.
+
+Depends: kalign
+Published-Title: Kalign--an accurate and fast multiple sequence alignment algorithm
+Published-Authors: Lassmann T, Sonnhammer EL.
+Published-In: BMC Bioinformatics, 6:298
+Published-Year: 2005
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16343337
+Published-PubMed: 16343337
+
+Depends: hmmer
+Published-Title: Multiple Alignment Using Hidden Markov Models.
+Published-Authors: S. R. Eddy.
+Published-In: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology, 114-120.
+Published-Year: 1995
+Published-URL: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf
+
+Depends: exonerate
+Published-Title: Automated generation of heuristics for biological sequence comparison
+Published-Authors: G.C. Slater, E. Birney
+Published-In: BMC Bioinformatics 6:31
+Published-Year: 2005
+Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
+Published-doi: 10.1186/1471-2105-6-31
+
+Depends: dialign
+Published-Authors: Burkhard Morgenstern
+Published-Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
+Published-In: Bioinformatics 15(3):211-218
+Published-Year: 1999
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10222408
+
+Depends: dialign-tx
+Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
+Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
+Published-In: Algorithms for Molecular Biology 3:6
+Published-Year: 2008
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568
+
+Depends: poa
+Published-Authors: C. Grasso, C. Lee
+Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
+Published-In: Bioinformatics 20(10):1546-1556.
+Published-Year: 2004
+
+Depends: probcons
+Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
+Published-In: Genome Research 15: 330-340
+Published-Year: 2005
+
+Depends: proda
+Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
+Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
+Published-In: Nucleic Acids Research 34(20), 5932-5942
+Published-Year: 2006
+
+Depends: seaview
+Published-Authors: N. Galtier, M. Gouy, C. Gautier
+Published-Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny
+Published-In: Comput. Applic. Biosci. 12:543-548
+Published-Year: 1996
+
+Depends: sigma-align
+X-Published-Authors: FIXME
+X-Published-Title: FIXME
+Published-In: BMC Bioinformatics 16;7:143
+Published-Year: 2006
+
+Depends: emboss
+Published-Authors: P. Rice, I. Longden, A. Bleasby
+Published-Title: EMBOSS: the European Molecular Biology Open Software Suite.
+Published-In: Trends Genet., 16(6):276-277
+Published-Year: 2000
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10827456
+
+Depends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
+Suggests:    emboss-explorer
+Why:         The EMBOSS sequence analysis suite and its galaxy.
+
+Depends:     arb
+Why:         Sequence alignments and related programs (Non-free, thus only suggested).
+
+Depends: clustalx, clustalo
+
+Depends: clustalw
+Published-Authors: M. Larkin, et al.
+Published-Title: Clustal W and Clustal X version 2.0
+Published-In: Bioinformatics 23(21):2947-2948
+Published-Year: 2007
+
+Depends: clustalw-mpi
+Comment: Originally the dependency was clustalw | clustalw-mpi but currently it is
+ not possible to specify an "OR relation" and tag the Published-* fields to only one
+ of them.
+
+Depends: mothur, bowtie, dotur
+
+Depends: transtermhp
+
+X-End-Category: Sequence alignments and related programs.
+
+X-Begin-Category: high-throughput sequencing
+
+Depends: last-align, maq, ssake, velvet
+
+Depends: qiime
+
+X-End-Category: high-throughput sequencing
+
+X-Begin-Category: Analysis of RNA sequences.
+
+Depends: infernal
+Published-Authors: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
+Published-Title: Infernal 1.0: inference of RNA alignments
+Published-In: Bioinformatics 15;25(10):1335-7
+Published-Year: 2009
+Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/full/25/10/1335
+
+Depends: rnahybrid
+Published-Authors: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann, Robert Giegerich
+Published-Title: Fast and effective prediction of microRNA/target duplexes RNA
+Published-In: 10:1507-1517
+Published-Year: 2004
+X-Category: Target duplex prediction
+
+X-End-Category: Analysis of RNA sequences.
+
+X-Begin-Category: Molecular modelling and molecular dynamics
+
+Depends:     adun.app
+Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator
+Published-Authors: M.A. Johnston, I.F. Galván, J. Villà -Freixa
+Published-In: J. Comp. Chem
+Published-Year: 2005
+Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT
+Published-DOI: 10.1002/jcc.20312
+
+Depends:     garlic, gamgi, gdpc, ghemical, jmol, pymol, r-other-bio3d, massxpert
+Comment:     r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team
+
+Depends: gromacs
+Published-Title: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
+Published-Authors: B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl
+Published-In: J. Chem. Theory Comput.
+Published-Year: 2008
+Published-URL: http://pubs.acs.org/doi/abs/10.1021/ct700301q
+Published-DOI: 10.1021/ct700301q
+X-Published-Other: Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis. J Mol Model. 2001;7(8):306.17.
+X-Published-Other: Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: Fast, Flexible, and Free. J Comput Chem. 2005;26(16):1701.18. [PubMed]
+
+Depends: rasmol
+Registration: http://www.rasmol.org/register.shtml
+Published-Title: RasMol: Biomolecular graphics for all
+Published-Authors: Roger Sayle and E. James Milner-White
+Published-In: Trends in Biochemical Sciences (TIBS)
+Published-Year: 1995
+
+X-End-Category: Molecular modelling and molecular dynamics
+
+Depends:     plasmidomics
+Why:         Presentation
+
+X-Begin-Category: Tools for the molecular biologist.
+
+Depends:     gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
+
+Depends: melting
+Published-Authors: Nicolas Le Novère
+Published-Title: MELTING, computing the melting temperature of nucleic acid duplex
+Published-In: Bioinformatics, 17: S.1226-1227
+Published-Year: 2001
+
+Suggests: melting-gui
+Comment: I think it makes sense to point users to GUI applications as well as to
+ the console applications - in this case melting (Andreas Tille)
+
+Depends: mipe
+Published-Authors: Aerts J & Veenendaal T.
+Published-Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
+Published-In: Online Journal of Bioinformatics 6(2): 114-120
+Published-Year: 2005
+
+Depends: primer3
+Published-Authors: S. Rozen, H. Skaletsky
+Published-Title: Primer3 on the WWW for general users and for biologist programmers
+Published-In: Methods Mol Biol. 132:365-86
+Published-Year: 2000
+
+X-End-Category: Tools for the molecular biologist.
+
+X-Begin-Category: Genome Browser
+
+Depends: gbrowse
+X-Importance: Academic ones are really expensive for commercial use
+
+X-End-Category: Genome Browser
+
+Depends: biomaj
+
+Suggests:    mozilla-biofox
+Why:         Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
+
+Depends:     glam2
+Why:         Motif search
+Published-Title: Discovering sequence motifs with arbitrary insertions and deletions
+Published-Authors: MC Frith, NFW Saunders, B Kobe, TL Bailey
+Published-In: PLoS Computational Biology
+Published-Year: 2008
+Published-DOI: 10.1371/journal.pcbi.1000071
+
+Depends: raster3d
+
+Depends: phyml
+
+Depends: autodock
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Why:         Molecular modelling and molecular dynamics.
+Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+Published-Authors: G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson
+Published-In: J. Comput. Chem.
+Published-Year: 2009
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
+Published-Pubmed: 19399780
+Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
+Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
+Published-In: Nucleic Acids Research 34(20), 5932-5942
+Published-Year: 2006
+
+Depends: autogrid
+
+Depends: autodock-vina
+
+Depends: autodocktools
+Comment: The package autodocktools depends from the mgltools-* packages mentioned
+         above, so they will be installed even if they would not be mentioned in
+         the list of Depends in the metapackage med-bio.  But leaving them out here
+         would hide them from the tasks and bugs list as well from the sectioning in
+         http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3
+         so they are mentioned here in addition to autodocktools.
+ .
+         This was changed by adding Enhances field to the packages in question.
+Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+Published-Authors: G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson
+Published-In: J. Comput. Chem.
+Published-Year: 2009
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
+
+Depends: mustang
+Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
+Published-Title: MUSTANG: A multiple structural alignment algorithm
+Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
+Published-Year: 2006
+
+Depends: theseus
+
+Depends: staden-io-lib-utils
+
+Depends: samtools, bedtools, filo
+
+Depends: gassst
+
+Depends: macs
+
+Depends: r-bioc-hilbertvis
+Published-Authors: Simon Anders
+Published-Title: Visualization of genomic data with the Hilbert curve
+Published-In: Bioinformatics 25(10):1231-1235
+Published-Year: 2009
+Published-DOI: 10.1093/bioinformatics/btp152
+Remark: It would be interesting to package HilbertVisGUI (see below) as well.
+
+Depends: r-other-mott-happy
+Published-Authors: Richard Mott, Christopher J. Talbot, Maria G. Turri, Allan C. Collins, Jonathan Flint
+Published-Title: A method for fine mapping quantitative trait loci in outbred animal stocks
+Published-In: Proc. Natl. Acad. Sci. USA
+Published-Year: 2000
+Published-DOI: 10.1073/pnas.230304397
+Remark: Do not upgrade this package
+ Steffen Möller is scientifically collaborating with upstream and nothing shall
+ happen to that package until authors give their confirmation.
+
+Depends: seq-gen
+
+Depends: mira-assembler
+Published-Title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
+Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.
+Published-In: Genome Res. Jun;14(6):1147-59.
+Published-Year: 2004
+Published-doi: 10.1101/gr.1917404
+Published-URL: http://pubmed.org/15140833
+
+Depends: bagphenotype
+Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
+License: GPL-3
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bagphenotype/bagphenotype/trunk/
+Pkg-Description: CLI for the bagphenotype R package
+ mapping QTLs in populations descended from known founders
+
+Depends: r-other-valdar-bagphenotype.library
+Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
+License: GPL-3
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-other-valdar-bagphenotype/trunk/
+Pkg-Description: GNU R extension of the functionality of happy
+ mapping QTLs in populations descended from known founders
+
+Depends: alien-hunter
+Published-Title: Interpolated variable order motifs for identification of horizontally acquired DNA:
+ revisiting the Salmonella pathogenicity islands
+Published-Authors: GS Vernikos and J. Parkhill
+Published-In: Bioinformatics
+Published-Year: 2006
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16837528
+Published-DOI: 10.1093/bioinformatics/btl369
+Published-PubMed: 16837528
+
+Suggests: seqan-apps
+
+Depends: ncoils
+
+Depends: gentle
+
+Depends: gmap
+Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences
+Published-Authors: Thomas D. Wu, Colin K. Watanabe
+Published-In: Bioinformatics
+Published-Year: 2005
+Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859
+
+Depends: igv
+
+Depends: picard-tools
+
+Depends: acedb-other-dotter, acedb-other-belvu, acedb-other
+
+Depends: python-cogent
+
+Depends: paml
+
+Depends: ensembl
+
+Depends: mrbayes
+
+Suggests: pdb2pqr
+
+Depends: squizz
+
+Depends: clonalframe
+
+Depends: jellyfish
+Published-Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
+Published-Authors: Guillaume Marcais and Carl Kingsford
+Published-In: Bioinformatics
+Published-Year: 2011
+Published-DOI: 10.1093/bioinformatics/btr011
+
+Depends: r-other-genabel
+Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
+Responsible: Steffen Moeller <steffen_moeller at gmx.de>
+License: GPL 2+
+WNPP: 492044
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-other-genabel/trunk/
+Pkg-Description: genome-wide SNP association analysis
+ A package for genome-wide association analysis between quantitative
+ or binary traits and single-nucleiotide polymorphisms (SNPs).
+
+Depends: meme
+Homepage: http://meme.nbcr.net/meme/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/meme/trunk/
+Pkg-Description: motif discovery and search
+ MEME is a tool for discovering motifs in a group of related DNA or protein
+ sequences.  A motif is a sequence pattern that occurs repeatedly in a group
+ of related protein or DNA sequences. MEME represents motifs as position-dependent
+ letter-probability matrices which describe the probability of each possible
+ letter at each position in the pattern. Individual MEME motifs do not contain
+ gaps. Patterns with variable-length gaps are split by MEME into two or more
+ separate motifs.
+ .
+ MEME takes as input a group of DNA or protein sequences (the training set)
+ and outputs as many motifs as requested. MEME uses statistical modeling
+ techniques to automatically choose the best width, number of occurrences,
+ and description for each motif.
+
+Depends: vienna-rna
+Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
+Responsible: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+License: non-free but redistributable
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/vienna-rna/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/vienna-rna/trunk/
+WNPP: 451193
+X-Category: Secondary structure of nucleic acids
+Pkg-Description: RNA sequence analysis
+ The Vienna RNA Package consists of a C code library and several
+ stand-alone programs for the prediction and comparison of RNA secondary
+ structures.
+
+Depends: cytoscape
+Homepage: http://cytoscape.org/
+Responsible: Mike Smoot <mes at aescon.com>
+License: LGPL
+WNPP: 465331
+Pkg-Description: visualizing molecular interaction networks
+ Cytoscape is a bioinformatics software platform for visualizing molecular
+ interaction networks and integrating these interactions with gene expression
+ profiles and other state data.  Additional features are available as plugins.
+
+Depends: ballview
+Published-Title: BALLView: a tool for research and education in molecular modeling.
+Published-Authors: A. Moll, A. Hildebrandt, H.P.Lenhof, O. Kohlbacher
+Published-In: Bioinformatics, 22(3):365-6
+Published-Year: 2006
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16332707
+
+Depends: python-pynast
+Published-Title: PyNAST: a flexible tool for aligning sequences to a template alignment
+Published-Authors: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
+Published-In: Bioinformatics 26: 266-267
+Published-Year: 2010
+Published-DOI: 10.1093/bioinformatics/btp636
+
+Depends: raxml
+
+Depends: mlv-smile
+
+Depends: axparafit
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+Responsible: David Paleino <d.paleino at gmail.com>
+License: GPL
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/axparafit/trunk/
+WNPP: 464323
+Pkg-Description: optimized statistical analysis of host-parasite coevolution
+ AxParafit is a highly optimized version of Pierre Legendre's Parafit
+ program for statistical analysis of host-parasite coevolution.
+ AxParafit has been parallelized with MPI (Message Passing Interface)
+ for compute clusters and was used to carry out the largest
+ co-evolutionary analysis to date for the paper describing the software.
+
+Depends: axpcoords
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+Responsible: David Paleino <d.paleino at gmail.com>
+License: GPL
+WNPP: 464323
+Pkg-Description: LAPACK-based implementation of DistPCoA
+ AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
+ http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
+ which is another program by Pierre Legendre, it conducts a principal
+ coordinates analysis.
+ This program is required for the pipeline that conducts a full host-parasite
+ co-phylogenetic analysis in combination with AxParafit.
+
+Depends: copycat
+Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
+License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
+Pkg-Description: fast access to cophylogenetic analyses
+ CopyCat provides an easy and fast access to cophylogenetic analyses.
+ It incorporates a wrapper for the program ParaFit, which conducts a
+ statistical test for the presence of congruence between host and
+ parasite phylogenies. CopyCat offers various features, such as the
+ creation of customized host-parasite association data and the
+ computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
+
+Depends: btk-core
+Homepage: http://sourceforge.net/projects/btk/
+Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
+License: GPL
+WNPP: 459753
+Pkg-Description: biomolecule Toolkit C++ library
+ The Biomolecule Toolkit is a library for modeling biological
+ macromolecules such as proteins, DNA and RNA. It provides a C++ interface
+ for common tasks in structural biology to facilitate the development of
+ molecular modeling, design and analysis tools.
+
+Depends: tacg
+Homepage: http://sourceforge.net/projects/tacg
+Responsible: Charles Plessy <plessy at debian.org>
+License: GPL and others
+WNPP: 461504
+X-Category: Motif detection
+X-Importance: powerful
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/tacg/trunk/
+Pkg-Description: command line program for finding patterns in nucleic acids
+ tacg is a character-based, command line tool for unix-like operating systems
+ for pattern-matching in nucleic acids and performing some of the basic protein
+ manipulations. It was originally designed for restriction enzyme analysis of
+ DNA, but has been extended to other types of matching. It now handles
+ degenerate sequence input in a variety of matching approaches, as well as
+ patterns with errors, regular expressions and TRANSFAC-formatted matrices.
+ .
+ It was designed to be a grep for DNA and like the original grep, its
+ capabilities have grown so that now the author has to keep calling up the help
+ page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
+ application in any sense. However, it's existance as a strictly command-line
+ tool lends itself well to Webification and wrapping by various GUI tools and
+ it is now distributed with a web interface form and a Perl CGI handler.
+ Additionally, it can easily be integrated into editors that support shell
+ commands such as nedit.
+ .
+ The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
+ BMC Bioinformatics. 3:8  http://www.biomedcentral.com/1471-2105/3/8
+
+Depends: treeplot
+Responsible: Charles Plessy <plessy at debian.org>
+License: GPL
+WNPP: 461508
+X-Category: Phylogenetic analysis
+X-Importance: Tree export to graphical formats
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treeplot
+Pkg-Description: Phylogenetic tree file converter
+ Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to
+ Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic
+ (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language
+ (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map
+ file (.pnm)
+ .
+ The upstream author Olivier Langella says: 'I think that "treeplot"
+ is outdated. "Treeviewx" is an equivalent that works great and it is
+ already packaged. ... you can replace "treeplot" with
+ "populations". I would be pleased if "populations" became a Debian
+ package.'  So this package should probably be delisted in favour of
+ populations (see http://lists.debian.org/debian-med/2008/03/msg00124.html).
+
+Depends: treevolve
+Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
+Responsible: Charles Plessy <plessy at debian.org>
+License: has to be verified
+WNPP: 461510
+Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treevolve
+Pkg-Description: simulation of evolution of DNA sequences
+ treevolve will simulate the evolution of DNA sequences under a
+ coalescent model, which allows exponential population growth,
+ population subdivision according to an island model, migration and
+ recombination. In addition different periods of population dynamics
+ can be enforced at different times. For example, a period of
+ exponential growth can be followed by a period of stasis where the
+ population is subdivided into demes. Multiple sets of such simulated
+ sequence data can then be compared to sequence data sampled from a
+ population of interest using suitable statistics, and various
+ evolutionary hypotheses concerning the evolution of this population
+ tested.
+ .
+ Citation: Population dynamics of HIV-1 inferred from gene sequences
+ Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
+
+Depends: asap
+Homepage: http://asap.ahabs.wisc.edu/software/asap/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Pkg-Description: organize the data associated with a genome
+ Developments in genome-wide approaches to biological research have
+ yielded greatly increased quantities of data, necessitating the cooperation
+ of communities of scientists focusing on shared sets of data. ASAP
+ leverages the internet and database technologies to meet these needs.
+ ASAP is designed to organize the data associated with a genome from the
+ early stages of sequence annotation through genetic and biochemical
+ characterization, providing a vehicle for ongoing updates of the annotation
+ and a repository for genome-scale experimental data. Development was
+ motivated by the need to more directly involve a greater community of
+ researchers, with their collective expertise, in keeping the genome
+ annotation current and to provide a synergistic link between up-to-date
+ annotation and functional genomic data. The system is continually under
+ development at the Genome Evolution Lab with the stable, in-use, publicly
+ available University of Wisconsin installation updated regularly.
+ .
+ Software development on ASAP began in early 2002, and ASAP has been
+ continually improved up until the present day. A longstanding goal of
+ the ASAP project was to make the source code of ASAP available so that
+ other installations of ASAP could be implemented. As future ASAP
+ installations come to pass, ASAP will be further extended to be
+ inter-operable between sites.
+X-Category: Annotation
+
+Depends: emboss-kaptain
+Homepage: http://userpage.fu-berlin.de/~sgmd/download.html
+Responsible: Charles Plessy <plessy at debian.org>
+License: GPL-2+
+WNPP: 466682
+Pkg-Description: graphical interface to EMBOSS using Kaptain
+ EMBOSS.kaptn is a graphical user interface (GUI) for more than 200
+ programms of the EMBOSS sequence analysis package. It uses Kaptain, a
+ universal front-end for command line applications. EMBOSS is a
+ collection of high-quality free Open Source software for sequence
+ analysis.  With EMBOSS.kaptn it integrates nicely into X window based
+ desktops like KDE.
+
+Depends: agdbnet
+Homepage: http://pubmlst.org/software/database/agdbnet/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+WNPP: 500106
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/agdbnet/trunk/
+Pkg-Description: antigen sequence database software for web-based bacterial typing
+ AgdbNet is antigen sequence database software for web-based bacterial
+ typing. The software facilitates simultaneous BLAST querying of multiple
+ loci using either nucleotide or peptide sequences. It's written in Perl
+ and runs on Linux/UNIX systems.
+ .
+ Databases are described by XML files and can have any number of loci, which
+ may be defined by nucleotide and/or peptide sequences. The databases can
+ optionally have integral isolate tables so that information about representative
+ isolates can be retrieved or they may be configured to query external isolate
+ databases, such as those hosted on PubMLST.org.
+ .
+ The software is used on a number of public bacterial typing databases:
+  * Neisseria PorA variable regions | PorB | FetA
+  * Campylobacter flaA
+  * Streptococcus equi seM
+
+Depends: martj
+Homepage: http://www.ebi.ac.uk/biomart/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/martj/trunk/
+Pkg-Description: distributed data integration system for biological data
+ BioMart is a simple, distributed data integration system with
+ powerful query capabilities. The BioMart data model has been applied
+ to the following data sources: UniProt Proteomes, Macromolecular
+ Structure Database (MSD), Ensembl, Vega, and dbSNP.
+
+Depends: cluster3
+Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
+License: non-free
+WNPP: 286167
+Responsible: Steffen Moeller <moeller at debian.org>
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cluster3/trunk/
+Pkg-Description: find clustering solutions for genome data
+ Cluster 3.0 is an enhanced version of Cluster, which was originally
+ developed by Michael Eisen while at Stanford University. The main
+ improvement consists of the k-means algorithm, which now includes
+ multiple trials to find the best clustering solution. This is crucial
+ for the k-means algorithm to be reliable. The routine for self-organizing
+ maps was extended to include 2D rectangular geometries. The Euclidean
+ distance and the city-block distance were added to the available
+ measures of similarity.
+
+Depends: jtreeview
+Homepage: http://jtreeview.sourceforge.net/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+WNPP: 243771
+X-Category: Visualisation
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/treeview/trunk/
+Pkg-Description: Java re-implementation of Michael Eisen's TreeView
+ TreeView creates a matrix-like display of expression data, known as
+ Eisen clustering. The original implementation was a Windows program
+ named TreeView by Michael Eisen. This TreeView package, sometimes also
+ referred to as jTreeView, was rewritten in Java under a free license,
+ the original implementation also comes with the source code, but controls
+ commercial distribution. And it did not run on Unix.
+ .
+ Java TreeView is an extensible viewer for microarray data in
+ PCL or CDT format.
+
+Depends: cactus
+Homepage: http://www.cactuscode.org/Community/Biology.html
+License: GPL
+Pkg-Description:
+ Cactus is an open source problem solving environment designed for scientists
+ and engineers. Its modular structure easily enables parallel computation
+ across different architectures and collaborative code development between
+ different groups.
+ .
+ Cactus provides easy access to many cutting edge software technologies being
+ developed in the academic research community, including the Globus
+ Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
+ adaptive mesh refinement, web interfaces, and advanced visualization tools.
+
+Depends: contralign
+Homepage: http://contra.stanford.edu/contralign/
+License: Public Domain
+Pkg-Description: parameter learning framework for protein pairwise sequence alignment
+ CONTRAlign is an extensible and fully automatic parameter learning
+ framework for protein pairwise sequence alignment based on pair
+ conditional random fields. The CONTRAlign framework enables the
+ development of feature-rich alignment models which generalize well to
+ previously unseen sequences and avoid overfitting by controlling model
+ complexity through regularization.
+
+Depends: galaxy
+Homepage: http://g2.trac.bx.psu.edu/
+License: MIT
+WNPP: 432472
+Pkg-Description: manipulate sequences and annotation files
+ Galaxy is a web-based tool allowing users to perform operations which
+ are usually done with command-line interface. Using galaxy, one can
+ manipulate sequences and annotation files in many formats. Galaxy has
+ strong ties with the UCSC genome browser, and makes it easy to
+ visualise modified annotation files as a custom track.
+
+Depends: genographer
+Homepage: http://hordeum.oscs.montana.edu/genographer/
+License: GPL
+Pkg-Description: read data and reconstruct them into a gel image
+ This program will read in data from an ABI 3700, 3100, 377 or 373,
+ CEQ 2000 or SCF and reconstruct them into a gel image which is
+ straightened and sized. Bins can be defined easily and viewed as
+ thumbnails, which allows for a fairly quick and easy way of scoring a gel.
+ .
+ The program is written in Java and uses the Java 1.3 API. Therefore,
+ it should run on any machine that can run java.
+
+Depends: molekel
+Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
+License: GPL
+Pkg-Description: multiplatform molecular visualization
+ Molekel is an opensource (GPL) multiplatform molecular visualization
+ program being developed at the Swiss National Supercomputing Centre
+ (CSCS).
+
+Depends: pftools
+Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
+License: GPL
+Pkg-Description: tools to handle patterns from PROSITE
+ ps_scan is a perl program used to scan one or several patterns, rules
+ and/or profiles from PROSITE against one or several protein sequences
+ in Swiss-Prot or FASTA format. It requires two compiled external
+ programs from the PFTOOLS, which are also distributed with the sources.
+
+Depends: proalign
+Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
+License: GPL
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 378290
+Pkg-Description: Probabilistic multiple alignment program
+ ProAlign performs probabilistic sequence alignments using hidden Markov
+ models (HMM). It includes a graphical interface (GUI) allowing to (i)
+ perform alignments of nucleotide or amino-acid sequences, (ii) view the
+ quality of solutions, (iii) filter the unreliable alignment regions and
+ (iv) export alignments to other softwares.
+ .
+ ProAlign uses a progressive method, such that multiple alignment is
+ created stepwise by performing pairwise alignments in the nodes of a
+ guide tree. Sequences are described with vectors of character
+ probabilities, and each pairwise alignment reconstructs the ancestral
+ (parent) sequence by computing the probabilities of different
+ characters according to an evolutionary model. It has been published in
+ Bioinformatics. 2003 Aug 12;19(12):1505-13.
+
+Depends: ssaha
+Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
+License: GPL
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 425111
+Pkg-Description: Sequence Search and Alignment by Hashing Algorithm
+ SSAHA is a software tool for very fast matching and alignment of DNA
+ sequences. It achieves its fast search speed by converting sequence
+ information into a `hash table' data structure, which can then be
+ searched very rapidly for matches. It was published by Ning Z,
+ Cox AJ, Mullikin JC in Genome Res. 2001;11;1725-9.
+ .
+ SSAHA is the only free software of its category (fast search of nearly
+ indentical sequences). The popular alternative, BLAT, is restricted to
+ non-commercial use.
+ .
+ Unfortunately the source of its successor ssaha2
+ http://www.sanger.ac.uk/Software/analysis/SSAHA2/
+ can not be relieased as Open Source because it contains
+ proprietary code.
+Remark: Successor for ssaha2 available: smalt
+ The program smalt is from the same author is according to its author
+ faster and more precise than ssaha2 (except for sequences > 2000bp)
+
+Depends: ngila
+Homepage: http://scit.us/projects/ngila/
+License: GPLv3
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 439996
+Pkg-Description: global pairwise alignments with logarithmic and affine gap costs
+ Ngila is an application that will find the best alignment of a pair
+ of sequences using log-affine gap costs, which are the most
+ biologically realistic gap costs.
+ .
+ Ngila implements the Miller and Myers (1988) algorithm in order to
+ find a least costly global alignment of two sequences given homology
+ costs and a gap cost. Two versions of the algorithm are
+ included: holistic and divide-and-conquer. The former is faster but
+ the latter utilizes less memory. Ngila starts with the
+ divide-and-conquer method but switches to the holistic method for
+ subsequences smaller than a user-established threshold. This improves
+ its speed without substantially increasing memory requirements. Ngila
+ also allows users to assign costs to end gaps that are smaller than
+ costs for internal gaps. This is important for aligning using the
+ free-end-gap method.
+ .
+ Ngila is published in Cartwright RA Bioinformatics 2007
+ 23(11):1427-1428; doi:10.1093/bioinformatics/btm095
+
+Depends: tm-align
+
+Depends: dazzle
+Homepage: http://www.biojava.org/dazzle
+Responsible: Steffen Moeller <moeller at debian.org>
+License: LGPL
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dazzle/trunk/
+Pkg-Description: Java-based DAS server
+ Dazzle is a general purpose server for the Distributed Annotation System
+ (DAS) protocol. It is implemented as a Java servlet, using the BioJava
+ APIs. Dazzle is a modular system which uses small "datasource" plugins to
+ provide access to a range of databases. Several general-purpose plugins
+ are included in the package, and it it straightforward to develop new
+ plugins to connect to your own databases.
+ .
+ Information on DAS is available from http://www.biodas.org/
+
+Depends: ecell
+Homepage: http://www.e-cell.org/
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 241195
+License: GPL
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ecell/trunk/
+Pkg-Description: Concept and environment for constructing virtual cells on computers
+ The E-Cell Project is an international research project aiming at
+ developing necessary theoretical supports, technologies and software
+ platforms to allow precise whole cell simulation.
+ .
+ The E-Cell System is an object-oriented software suite for modeling,
+ simulation, and analysis of large scale complex systems such as
+ biological cells, architected by Kouichi Takahashi and written by
+ a team of developers.
+ .
+ The core part of the system, E-Cell Simulation Environment version 3,
+ allows many components driven by multiple algorithms with different
+ timescales to coexist.
+ .
+ E-Cell System consists of the following three major parts:
+  * E-Cell Simulation Environment (or E-Cell SE)
+  * E-Cell Modeling Environment (or E-Cell ME)
+  * E-Cell Analysis Toolkit.
+
+Depends: haploview
+Homepage: http://www.broad.mit.edu/mpg/haploview/
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 311421
+License: DFSG free
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/haploview/trunk/
+Pkg-Description: Analysis and visualization of LD and haplotype maps
+ This tools assists in the analysis of the nucleotide
+ variation in a population. Such investigations are performed
+ to determine genes and genetic pathways that are associated
+ with diseases. This is an early stage in the quest for new drugs.
+
+Depends: bio-mauve
+Homepage: http://asap.ahabs.wisc.edu/mauve/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Language: C++ and Java
+X-Category: Multiple genome alignment
+X-Importance: efficient
+Pkg-Description: multiple genome alignment
+ Mauve is a system for efficiently constructing multiple genome alignments
+ in the presence of large-scale evolutionary events such as rearrangement
+ and inversion. Multiple genome alignment provides a basis for research
+ into comparative genomics and the study of evolutionary dynamics.  Aligning
+ whole genomes is a fundamentally different problem than aligning short
+ sequences.
+ .
+ Mauve has been developed with the idea that a multiple genome aligner
+ should require only modest computational resources. It employs algorithmic
+ techniques that scale well in the amount of sequence being aligned. For
+ example, a pair of Y. pestis genomes can be aligned in under a minute,
+ while a group of 9 divergent Enterobacterial genomes can be aligned in
+ a few hours.
+ .
+ Mauve computes and interactively visualizes genome sequence comparisons.
+ Using FastA or GenBank sequence data, Mauve constructs multiple genome
+ alignments that identify large-scale rearrangement, gene gain, gene loss,
+ indels, and nucleotide substutition.
+ .
+ Mauve is developed at the University of Wisconsin.
+ .
+ Note: There are instructions for compiling Mauve from source available at
+ http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html
+
+Depends: mauvealigner
+Homepage: http://asap.ahabs.wisc.edu/mauve/
+Responsible: Andreas Tille <tille at debian.org>
+License: GPL
+Pkg-URL: http://people.debian.org/~tille/packages/mauvealigner/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mauvealign/trunk/
+Pkg-Description: multiple genome alignment algorithms
+ The mauveAligner and progressiveMauve alignment algorithms have been
+ implemented as command-line programs included with the downloadable Mauve
+ software.  When run from the command-line, these programs provide options
+ not yet available in the graphical interface.
+ .
+ Mauve is a system for efficiently constructing multiple genome alignments
+ in the presence of large-scale evolutionary events such as rearrangement
+ and inversion. Multiple genome alignment provides a basis for research
+ into comparative genomics and the study of evolutionary dynamics.  Aligning
+ whole genomes is a fundamentally different problem than aligning short
+ sequences.
+ .
+ Mauve has been developed with the idea that a multiple genome aligner
+ should require only modest computational resources. It employs algorithmic
+ techniques that scale well in the amount of sequence being aligned. For
+ example, a pair of Y. pestis genomes can be aligned in under a minute,
+ while a group of 9 divergent Enterobacterial genomes can be aligned in
+ a few hours.
+ .
+ Mauve computes and interactively visualizes genome sequence comparisons.
+ Using FastA or GenBank sequence data, Mauve constructs multiple genome
+ alignments that identify large-scale rearrangement, gene gain, gene loss,
+ indels, and nucleotide substutition.
+ .
+ Mauve is developed at the University of Wisconsin.
+
+Depends: phylographer
+Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
+License: GPL
+X-Category: Graphical representation of sequence conservation
+Language: Tcl/Tk
+Pkg-Description: Graph Visualization Tool
+ PhyloGrapher is a program designed to visualize and study evolutionary
+ relationships within families of homologous genes or proteins
+ (elements).  PhyloGrapher is a drawing tool that generates custom graphs
+ for a given set of elements. In general, it is possible to use
+ PhyloGrapher to visualize any type of relations between elements.
+ Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
+ the results of a BLAST search as a graph.
+ .
+ PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
+ biological sequence alignment reports (BLAST is provided by Debian's
+ blast2 package).
+Remark: Outdated upstream, better alternatives available
+ The former packaging effort of this package was dropped.  It seems
+ that http://cytoscape.org/ is a reasonable replacement.
+
+Depends: phylowin
+Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
+WNPP: 395840
+License: unknown
+Pkg-Description: Graphical interface for molecular phylogenetic inference
+ Phylo_win is a graphical colour interface for molecular phylogenetic
+ inference. It performs neighbor-joining, parsimony and maximum
+ likelihood methods and bootstrap with any of them. Many distances can be
+ used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
+ (1995), LogDet for nucleotidic sequences, Poisson correction for protein
+ sequences, Ka and Ks for codon sequences. Species and sites to include
+ in the analysis are selected by mouse. Reconstructed trees can be drawn,
+ edited, printed, stored and evaluated according to numerous criteria.
+ .
+ This program uses sources files from the Phylip program, which forbids
+ its use for profit.  Therfore, Phylo_win will unfortunately have to be
+ distributed in contrib or non-free.
+Remark: Issuer of previous ITP said:
+ Because I could never figure out the license of Phylo_win, and because the
+ upstream authors released SeaView 4, which provides similar functionalities, I
+ will not package Phylo_win.
+ .
+ Probably it makes sense to remove this project from the prospective packages
+ list.
+
+Depends: wgs-assembler
+Homepage: http://wgs-assembler.sourceforge.net/
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 395843
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wgs-assembler/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wgs-assembler/trunk/
+License: GPL
+Pkg-Description: Whole-Genome Shotgun Assembler
+ Celera Assembler is scientific software for DNA research. It can
+ reconstruct long sequences of genomic DNA given the fragmentary data
+ produced by whole-genome shotgun sequencing. The Celera Assembler
+ enabled many advances in genomics, including the first genome
+ sequence of a multi-cellular organism and the first diploid sequence
+ of an individual human.
+ .
+ The Celera Assembler is a member of a class of software called
+ whole-genome shotgun assemblers. The Celera Assembler is mature,
+ efficient, open-source software with a long record of contributions
+ to science. Celera Assembler is written mostly in C for unix
+ operating systems. Although it requires large compute resources to
+ resolve complex genomes, it can assemble bacterial genomes on a
+ laptop.
+ .
+ This important software is an "open source" project. Originally
+ developed at Celera Genomics, it was released under the GNU Public
+ License and deposited on a public repository (Source Forge) in
+ 2004. Scientists around the world can download, build, and run the
+ software without restriction. In addition, they can inspect the
+ source code and alter it at their own sites. Workers at JCVI and a
+ few other institutes regularly submit their code alterations to the
+ public repository.
+ .
+ JCVI has made many important contributions to Celera
+ Assembler. Scientists and engineers at JCVI are extending the code to
+ handle more and more polymorphic data sets, including environmental
+ samples. In collaboration with scientists at the University of
+ Maryland, they are adding the capability to assemble pyrosequencing
+ data (as from a 454 FLX machine) in addition to the traditional
+ Sanger sequencing data (as from an ABI 3730 machine). JCVI's efforts
+ provide the cutting edge software that genome scientists around the
+ world will need as they apply DNA sequencing technology to more and
+ more difficult problems of biology.
+ .
+ See also: http://www.jcvi.org/cms/research/software/celera-assembler/overview/
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: gbioseq
+Homepage: http://www.bioinformatics.org/project/?group_id=94
+License: GPL
+Pkg-Description: DNA sequence editor for Linux
+ gBioSeq is in an early stage of development, but it is already running.
+ The goal is to provide an easy to use software to edit DNA sequences under
+ Linux, Windows, MacOsX, using GTK C# (Mono).
+
+Depends: phpphylotree
+Homepage: http://www.bioinformatics.org/project/?group_id=372
+License: GPL
+Pkg-Description: draw phylogenetic trees
+ PhpPhylotree is a web application that is able to draw phylogenetic trees.
+ It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
+
+Depends: tracetuner
+Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview
+License: GPL; but US Patent #6,681,186
+Pkg-Description: DNA sequencing and trace processing
+ TraceTuner is a DNA sequencing quality value, base calling and trace
+ processing software application originally developed by Paracel,
+ Inc. While providing a flexible interface and capability to adopt the
+ "pure" base calls produced by Phred, KB or any other "original"
+ caller, it offers competitive features not currently available in
+ other tools, such as customized calibration of quality values,
+ advanced heterozygote and mixed base calling and deconvolving the
+ "mixed" electropherograms resulting from the presence of indels into
+ a couple of "pure" electropherograms. Previous versions of TraceTuner
+ were used by Celera Genomics to process over 27 million reads from
+ both Drosophila and human genome projects and by Applied Biosystems,
+ as a component of its SNP detection and genotyping software product
+ SeqScape. TraceTuner implements an advanced peak processing
+ technology for resolving overlapping peaks of the same dye color into
+ individual, or "intrinsic" peaks. This technology was protected by US
+ Patent #6,681,186. Currently, TraceTuner is an open source software,
+ which has been used by J. Craig Venter Institute's DNA Sequencing and
+ Resequencing pipelines.
+ .
+ The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All
+ rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is
+ being made available free of charge by Applera Corporation subject to the terms
+ and conditions of the GNU General Public License, version 2, as published by the
+ Free Software Foundation (the "GNU General Public License").
+
+Depends: twain
+Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
+License: Open Source
+Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
+ TWAIN is a new syntenic genefinder which employs a Generalized Pair
+ Hidden Markov Model (GPHMM) to predict genes in two closely related
+ eukaryotic genomes simultaneously.  It utilizes the MUMmer package to
+ perform approximate alignment before applying a GPHMM based on an
+ enhanced version of the TigrScan gene finder.  TWAIN was written by
+ Bill Majoros and Mihaela Pertea while at The Institute for Genomic
+ Research (TIGR).
+ .
+ TWAIN consists of two components: (1) ROSE, the Region Of Synteny
+ Extractor, which identifies contiguous regions likely to contain one
+ or more syntenic genes, and (2) OASIS, a generalized pair hidden
+ Markov model (GPHMM) for predicting genes in the regions identified
+ by ROSE.  The system utilizes approximate alignments constructed by
+ the PROmer and NUCmer programs in the MUMmer package to assess
+ approximate alignment scores efficiently.  More detailed information
+ on the architecture of this system will be made available soon.
+ Slides from a talk at Computational Genomics 2004 are now available.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: rose
+Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
+License: Open Source
+Pkg-Description: Region-Of-Synteny Extractor
+ ROSE is a program which identifies regions between two genomes which
+ are likely to contain orthologous genes. The two genomes are given as
+ two multi fasta files of DNA sequences. The PROmer program from the
+ MUMmer package needs to be run first between the two genomes, and the
+ resulting delta file is then input to ROSE. If a previous annotation
+ is available for one or both genomes, then the coordinates of the
+ annotated genes from a genome can be optionally given as input in a
+ gff file. The gene coordinates will be used to guide the length of
+ the regions produced by ROSE. By default, when finding a region of
+ consistent alignments, ROSE will add a user-defined margin (1000 bp
+ by default) on either side of that region. When a predicted gene
+ overlaps an alignment we use the gene prediction to extend the
+ boundaries of the output region.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: glimmerhmm
+Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
+License: Artistic
+Pkg-Description: Eukaryotic Gene-Finding System
+ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
+ Model (GHMM). Although the gene finder conforms to the overall
+ mathematical framework of a GHMM, additionally it incorporates splice
+ site models adapted from the GeneSplicer program and a decision tree
+ adapted from GlimmerM. It also utilizes Interpolated Markov Models
+ for the coding and noncoding models . Currently, GlimmerHMM's GHMM
+ structure includes introns of each phase, intergenic regions, and
+ four types of exons (initial, internal, final, and single). A basic
+ user manual can be consulted here.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: genezilla
+Homepage: http://www.genezilla.org/
+License: Artistic
+Language: C++
+X-Importance: state-of-art
+X-Category: Gene prediction (through GHMM)
+Pkg-Description: eukaryotic gene finder
+ GeneZilla is a state-of-the-art program for computational prediction
+ of protein-coding genes in eukaryotic DNA, and is based on the
+ Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
+ and GENIE. It is highly reconfigurable and includes software for
+ retraining by the end-user. It is written in highly optimized C++ and
+ runs under most UNIX/Linux platforms. The run time and memory
+ requirements are linear in the sequence length, and are in general
+ much better than those of competing systems, due to GeneZilla's novel
+ decoding algorithm. Graph-theoretic representations of the high
+ scoring open reading frames are provided, allowing for exploration of
+ sub-optimal gene models. It utilizes Interpolated Markov Models
+ (IMMs), Maximal Dependence Decomposition (MDD), and includes states
+ for signal peptides, branch points, TATA boxes, CAP sites, and will
+ soon model CpG islands as well.
+ .
+ GeneZilla is an open-source project hosted at bioinformatics.org and
+ currently consists of ~20,000 lines of code.  GeneZilla evolved out
+ of the ab initio eukaryotic gene finder TIGRscan, which was developed
+ at The Institute for Genomic Research over a 3-year period under NIH
+ grants R01-LM06845 and R01-LM007938, and which served as the basis
+ for the comparative gene finder TWAIN.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: exalt
+Homepage: http://www.cbcb.umd.edu/software/exalt/
+License: Artistic
+Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
+ ExAlt is a software program designed to predict alternatively spliced
+ overlapping exons in genomic sequence. The program works in several
+ ways depending on the available input. ExAlt can use information of
+ existing gene structure as well as sequence conservation to improve
+ the precision of it's predictions. ExAlt can also make predictions
+ when only a single genomic sequence is available. ExAlt has been
+ extensively tested on Drosophila melanogaster, but can be adapted to
+ run on other species.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: jigsaw
+Homepage: http://www.cbcb.umd.edu/software/jigsaw/
+License: Artistic
+Pkg-Description: gene prediction using multiple sources of evidence
+ JIGSAW is a program designed to use the output from gene finders,
+ splice site prediction programs and sequence alignments to predict
+ gene models. The program provides an automated way to take advantage
+ of the many succsessful methods for computational gene prediction and
+ can provide substantial improvements in accuracy over an individual
+ gene prediction program.
+ .
+ JIGSAW is available for all species. It is tested on Human, Rice
+ (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
+ neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
+ fumigatus, Plasmodium falciparum and Plasmodium yoelii.
+ .
+ The linear combiner option is now available in the current JIGSAW
+ software distribution. This allows JIGSAW to be run without the use
+ of training data. A weight is assigned to each evidence source, and
+ gene predictions are based on a weighted voting scheme, yielding the
+ best 'consensus' predictions.
+ .
+ Predictions are now available for the ENCODE regions in Human and
+ viewable as custom tracks in the UCSC Human Genome
+ Browser. Predictions available for the Human genome and viewable as
+ custom tracks in the UCSC Human Genome Browser
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Depends: genesplicer
+Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
+License: Artistic
+Pkg-Description: computational method for splice site prediction
+ A fast, flexible system for detecting splice sites in the genomic DNA
+ of various eukaryotes. The system has been trained and tested
+ successfully on Plasmodium falciparum (malaria), Arabidopsis
+ thaliana, human, Drosophila, and rice . Training data sets for human
+ and Arabidopsis thaliana are included. Use the GeneSplicer Web
+ Interface to run GeneSplicer directly, or see below for instructions
+ on downloading the complete system including source code.
+ .
+ There is no independent program to train GeneSplicer, but there is a
+ way to obtain the necessary files by using the training procedure of
+ GlimmerHMM.
+Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
+
+Ignore: riso
+Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
+License: not specified
+Pkg-Description: motif discovery tool
+ RISO discovers motifs composed of many binding sites separated by
+ spacers. Each binding site is called a box
+ .
+ The author of SMILE claims at his homepage
+ http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is
+ faster and more powerfull than SMILE which is described itself as
+ "SMILE is a tool that infers motifs in a set of sequences, according
+ to some criterias. It was first made to infer exceptionnal sites as
+ binding sites in DNA sequences. It allows to infer motifs written on
+ any alphabet (even degenerate) in any kind of sequences.  The
+ specificity of SMILE is to allow  to deal with what we call
+ "structured motifs",  which are motifs associated by some distance
+ constraints. In particular, SMILE is able to group under a unique
+ model different occurrences composed of several boxes separated by
+ spacers of different lengths."
+ .
+ The reference to SMILE is made here especially because there is some
+ work done in the Debian Med SVN at
+ http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/
+ .
+ On the other hand the SMILE author told us in private mail that he
+ thinks that RISO is dead and SMILE continues to have some importance.
+
+Depends: mummergpu
+Homepage: http://mummergpu.sourceforge.net/
+License: Artistic
+Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
+ The recent availability of new, less expensive high-throughput DNA
+ sequencing technologies has yielded a dramatic increase in the volume
+ of sequence data that must be analyzed. These data are being
+ generated for several purposes, including genotyping, genome
+ resequencing, metagenomics, and de novo genome assembly
+ projects. Sequence alignment programs such as MUMmer have proven
+ essential for analysis of these data, but researchers will need ever
+ faster, high-throughput alignment tools running on inexpensive
+ hardware to keep up with new sequence technologies.
+ .
+ MUMmerGPU is a low cost, ultra-fast sequence alignment program
+ designed to handle the increasing volume of data produced by new,
+ high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in
+ replacement for MUMmer, using the GPUs in common workstations to
+ simultaneously align multiple query sequences against a single
+ reference sequence stored as a suffix tree. By processing the queries
+ in parallel on the highly parallel graphics card, MUMmerGPU achieves
+ more than a 10-fold speedup over a serial CPU version of the sequence
+ alignment kernel, and outperforms MUMmer on a high end CPU by
+ 3.5-fold in total application time when aligning reads from recent
+ sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
+ technologies.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: amos-assembler
+Homepage: http://amos.sourceforge.net/
+License: Artistic
+Language: Perl
+X-Category: Genome assembling
+Pkg-Description: modular whole genome assembler
+ The AMOS consortium is committed to the development of open-source
+ whole genome assembly software. The project acronym (AMOS) represents
+ our primary goal -- to produce A Modular, Open-Source whole genome
+ assembler. Open-source so that everyone is welcome to contribute and
+ help build outstanding assembly tools, and modular in nature so that
+ new contributions can be easily inserted into an existing assembly
+ pipeline. This modular design will foster the development of new
+ assembly algorithms and allow the AMOS project to continually grow
+ and improve in hopes of eventually becoming a widely accepted and
+ deployed assembly infrastructure. In this sense, AMOS is both a
+ design philosophy and a software system.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: amoscmp
+Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
+License: Artistic
+Pkg-Description: comparative genome assembly package
+ A comparative assembler is a program that can assemble a set of
+ shotgun reads from an organism by mapping them to the finished
+ sequence of a related organism. Thus, a comparative assembler
+ transforms the traditional overlap-layout-consensus approach to
+ alignment-layout-consensus. The AMOScmp package uses the MUMmer
+ program to perform a mapping of the reads to the reference genome,
+ then processes the alignment results with a sophisticated layout
+ program designed to take into account polymorphisms between the two
+ genomes. For a detailed description of the algorithms involved please
+ refer to the paper listed in the References section.
+ .
+ AMOScmp uses as AMOS messages as both the inputs and the outputs (see
+ documentation). Two utilities are provided to process these files:
+ tarchive2amos - a versatile converter from trace archive .seq, .qual,
+ and .xml information into AMOS formatted data; amos2ace - a converter
+ from AMOS formatted data to the .ACE assembly format. In addition,
+ the AMOS::AmosLib Perl module is provided as a tool for users who
+ prefer to write their own conversion utilities. Please see the
+ documentation included with the distribution for more information.
+ .
+ AMOScmp is part of the AMOS package (see
+ http://amos.sourceforge.net/)- a collaborative effort to develop a
+ modular open-source framework for assembly development.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: minimus
+Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
+License: Artistic
+Pkg-Description: AMOS lightweight assembler
+ minimus is an assembly pipeline designed specifically for small
+ data-sets, such as the set of reads covering a specific gene. Note
+ that the code will work for larger assemblies (we have used it to
+ assemble bacterial genomes), however, due to its stringency, the
+ resulting assembly will be highly fragmented. For large and/or
+ complex assemblies the execution of Minimus should be followed by
+ additional processing steps, such as scaffolding.
+ .
+ minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
+  * overlapper - computes the overlaps between the reads using a
+    modified version of the Smith-Waterman local alignment algorithm
+  * tigger - uses the read overlaps to generate the layouts of reads
+    representing individual contigs
+  * make-consensus - refines the layouts produced by the tigger to
+    generate accurate multiple alignments within the reads
+ .
+ minimus uses as AMOS messages as both the inputs and the outputs (see
+ documentation). Two utilities are provided to process these files:
+ tarchive2amos - a versatile converter from trace archive .seq, .qual,
+ and .xml information into AMOS formatted data; amos2ace - a converter
+ from AMOS formatted data to the .ACE assembly format. In addition,
+ the AMOS::AmosLib Perl module is provided as a tool for users who
+ prefer to write their own conversion utilities. Please see the
+ documentation included with the distribution for more information.
+ .
+ minimus is part of the AMOS package - a collaborative effort to
+ develop a modular open-source framework for assembly development.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Ignore: catissuecore
+Homepage: https://cabig.nci.nih.gov/tools/catissuecore
+License: to be clarified, NCICB Open Source Project Site
+Pkg-Description: biospecimen inventory, tracking, and basic annotation
+ caTissue Core is caBIG's tissue bank repository tool for biospecimen
+ inventory, tracking, and basic annotation. Version 1.2.1 of caTissue
+ permits users to track the collection, storage, quality assurance,
+ and distribution of specimens as well as the derivation and
+ aliquotting of new specimens from an existing ones (e.g. for DNA
+ analysis). It also allows users to find and request specimens that
+ may then be used in molecular, correlative studies.
+ .
+ Intended Audiences: Translational Researchers, Pathologists, Biobank
+ Managers
+Note: A lot of stuff can be found at National Cancer Institute's
+ Center for Bioinformatics (NCICB) Open Source Project Site
+ http://gforge.nci.nih.gov/ which has to be evaluated and put into the
+ right category of our tasks files
+
+Ignore: trapss
+Homepage: https://putt.eng.uiowa.edu/
+License: Creative Commons for Science license
+Pkg-Description: Transcript Annotation Prioritization and Screening System
+ TrAPSS stands for Transcript Annotation Prioritization and Screening
+ System. It is a system comprised of several tools written by
+ researchers at the Coordinated Lab for Computational Genomics in the
+ University of Iowa. The system aims to aid scientists who are
+ searching for the genetic mutation or mutations that are linked to
+ expression of a disease phentotype. The system offers support for
+ almost all areas of a mutation discovery project from the creation
+ and prioritization of a large candidate gene list, to the selection,
+ ordering, and managing of primer pairs, and even support for SSCP
+ assay results. TrAPSS is a currently deployed and often used tool for
+ several laboratories here at the University of Iowa in the College of
+ Medicine. The system is composed of several Java applications, many
+ web-based PHP tools, and a local MySQL database. Even the Java
+ applications are available through a web browser due to Sun's Java
+ Web Start. Director of the CLCG, Professor Terry A. Braun, heads the
+ project along with Dr. Todd Scheetz and Prof. Thomas
+ L. Casavant. Eight developers create and maintain the software:
+ Bartley Brown , Hakeem Almabrazi, Steven Davis and Jason Grundstad;
+ along with three graduate students, Brian O'Leary, John Ritchison and
+ Michael Smith; and one undergraduate student, Matthew Kemp.
+ Importance of TrAPSS
+ .
+ The true importance of TrAPSS is that it is based upon a novel way to
+ examine a large candidate list of genes. Rather than sequentially
+ examining full genes, the scheme often followed in current target
+ identification projects, TrAPSS provides tools that offer the user
+ the opportunity to screen certain small parts of several genes from
+ the candidate list at once. This "parallel" screening idea was
+ envisioned by researchers here at the University of Iowa including
+ Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate
+ students Steven Davis and Brian O'Leary has demonstrated the
+ advantage of the parallel screening method over the sequential
+ sequencing of large candidate lists.
+Note: Found at
+ http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
+
+Depends: mage2tab
+Homepage: https://www.cbil.upenn.edu/magewiki/index.php/mage2tab
+License: CBIL Software and Data License (Apache-like)
+WNPP: 476209
+Responsible: Charles Plessy <plessy at debian.org>
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mage2tab/trunk/
+Pkg-Description: MAGE-MLv1 converter and visualiser
+ This tool-kit is part of MR_T, a framework for import or export various of
+ MAGE (MicroArray Gene Expression) documents (MAGE-MLv1, MAGE-TAB, SOFT,
+ MINiML) from or into databases like GUS (the Genomics Unified Schema,
+ www.gusdb.org).
+
+Depends: bambus
+Homepage: http://amos.sourceforge.net/docs/bambus/
+License: Artistic
+Pkg-Description: hierarchical approach to building contig scaffolds
+ BAMBUS is the first publicly available scaffolding program. It orders
+ and orients contigs into scaffolds based on various types of linking
+ information. Additionally, BAMBUS allows the users to build scaffolds
+ in a hierarchical fashion by prioritizing the order in which links
+ are used. For more information please check out the online
+ documentation.
+ .
+ Note that currently Bambus is undergoing a transition in order to be
+ integrated with the AMOS package (see http://amos.sourceforge.net/)
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: hawkeye
+Homepage: http://amos.sourceforge.net/hawkeye/
+License: Artistic
+Pkg-Description: Interactive Visual Analytics Tool for Genome Assemblies
+ Genome assembly remains an inexact science. Even when accomplished
+ with the best software available, the assembly of a genome often
+ contains numerous errors, both small and large. Hawkeye is a visual
+ analytics tool for genome assembly analysis and validation, designed
+ to aid in identifying and correcting assembly errors. Hawkeye blends
+ the best practices from information and scientific visualization to
+ facilitate inspection of large-scale assembly data while minimizing
+ the time needed to detect mis-assemblies and make accurate judgments
+ of assembly quality.
+ .
+ All levels of the assembly data hierarchy are made accessible to
+ users, along with summary statistics and common assembly metrics. A
+ ranking component guides investigation towards likely mis-assemblies
+ or interesting features to support the task at hand. Wherever
+ possible, high-level overviews, dynamic filtering, and automated
+ clustering are leveraged to focus attention and highlight anomalies
+ in the data. Hawkeyes effectiveness has been proven on several genome
+ projects, where it has been used both to improve quality and to
+ validate the correctness of complex genomes.
+ .
+ Hawkeye is compatible with most widely used assemblers, including
+ Phrap, ARACHNE, Celera Assembler, Newbler, AMOS, and assemblies
+ deposited in the NCBI Assembly Archive.
+ .
+ Publication: Schatz, M.C., Phillippy, A.M., Shneiderman, B.,
+ Salzberg, S.L. (2007) Hawkeye: a visual analytics tool for genome
+ assemblies. Genome Biology 8:R34.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: murasaki
+Homepage: http://murasaki.dna.bio.keio.ac.jp/
+License: GPL
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/murasaki/trunk/
+Pkg-Description: homology detection tool across multiple large genomes
+ Murasaki is a scalable and fast, language theory-based homology
+ detection tool across multiple large genomes. It enable whole-genome
+ scale multiple genome global alignments. Supports unlimited length
+ gapped-seed patterns and unique TF-IDF based filtering.
+ .
+ Murasaki is an anchor alignment software, which is
+  * exteremely fast (17 CPU hours for whole Human x Mouse genome (with
+    40 nodes: 52 wall minutes))
+  * scalable (Arbitrarily parallelizable across multiple nodes using MPI.
+    Even a single node with 16GB of ram can handle over 1Gbp of sequence.)
+  * unlimited pattern length
+  * repeat tolerant
+  * intelligent noise reduction
+
+Depends: gmv
+Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
+License: GPL
+Pkg-Description: comparative genome browser for Murasaki
+ GMV is a comparative genome browser for Murasaki. GMV visualizes
+ anchors from Murasaki, annotation data from GenBank files, and
+ expression / prediction score from GFF files.
+
+Depends: pyrophosphate-tools
+Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html
+License: not specified
+Pkg-Description: for assembling and searching pyrophosphate sequence data
+ Simple tools for assembling and searching high-density picolitre
+ pyrophosphate sequence data.
+
+Depends: figaro
+Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
+License: Artistic
+Pkg-Description: novel vector trimming software
+ Figaro is a software tool for identifying and removing the vector
+ from raw DNA sequence data without prior knowledge of the vector
+ sequence.  By statistically modeling short oligonucleotide
+ frequencies within a set of reads, Figaro is able to determine which
+ DNA words are most likely associated with vector sequence.  For a
+ description of Figaro's algorithms please see our paper.  Figaro is
+ part of the AMOS suite.
+Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
+
+Depends: mirbase
+Homepage: http://microrna.sanger.ac.uk/
+License: Public Domain
+WNPP: 420938
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: The microRNA sequence database
+ The miRBase Sequence Database provides a searchable repository
+ for published microRNA sequences and associated annotation,
+ functionality previously provided by the microRNA Registry.  miRBase
+ also contains predicted miRNA target genes in miRBase Targets, and
+ provides a gene naming and nomenclature function in the miRBase
+ Registry.
+ .
+ Release 9.1 of the database contains 4449 entries representing hairpin
+ precursor miRNAs, expressing 4274 mature miRNA products, in primates,
+ rodents, birds, fish, worms, flies, plants and viruses.
+ .
+ This package will install the miRBase database for mySQL, EMBOSS, and/or
+ ncbi-blast if you have the corresponding packages installed.
+ .
+ It is possible that mirbase will not be a package from the main archive, but
+ will be autogenerated as part of a larger data packaging effort.
+
+Depends: elph
+Homepage: http://www.cbcb.umd.edu/software/ELPH/
+License: Artistic
+Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
+ ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs
+ sampler for finding motifs in a set of DNA or protein sequences. The
+ program takes as input a set containing anywhere from a few dozen to
+ thousands of sequences, and searches through them for the most common
+ motif, assuming that each sequence contains one copy of the motif. We
+ have used ELPH to find patterns such as ribosome binding sites (RBSs)
+ and exon splicing enhancers (ESEs). See below for instructions on
+ downloading the complete system, including source code.
+ .
+ An online tool that uses ELPH output for identifying exon splicing
+ enhancers can be found at
+ http://www.cbcb.umd.edu/software/SeeEse/index.html .
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: repeatfinder
+Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
+License: Artistic
+Pkg-Description: finding repetitive sequences complete and draft genomes
+ Two programs for finding repeats in genomic DNA sequences.  The first
+ program, described in the paper by Volfovsky et al. (2001) Genome
+ Biology is RepeatFinder.  A second program, designed specifically to
+ find repeats likely to confuse a genome assembly, is called
+ ClosureRepeatFinder.  The two programs are quite different and have
+ different purposes; RepeatFinder is intended to be the more
+ comprehensive approach.  Note that RepeatFinder depends on Stefan
+ Kurtz's REPuter.
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
+
+Depends: reputer
+Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
+License: to be clarified
+Pkg-Description: fast computation of maximal repeats in complete genomes
+ A software tool was implemented that computes exact repeats and
+ palindromes in entire genomes very efficiently.
+Note: Download site (temporarily) not available - try to contact author
+
+Depends: patman
+Homepage: http://bioinf.eva.mpg.de/patman/
+License: GPL-2+
+WNPP: 482555
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: rapid alignment of short sequences to large databases
+ Patman searches for short patterns in large DNA databases, allowing
+ for approximate matches. It is optimized for searching for many small
+ pattern at the same time, for example microarray probes.
+
+Depends: uniprime
+Homepage: http://code.google.com/p/uniprime/
+License: GPL-3+
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: workflow-based platform for universal primer design
+ UniPrime automatically designs large sets of universal primers by simply
+ inputting a GeneID reference. It automatically retrieves and aligns
+ orthologous sequences from GenBank, identifies regions of conservation within
+ the alignment and generates suitable primers that can amplify variable genomic
+ regions. UniPrime differs from previous automatic primer design programs in
+ that all steps of primer design are automated, saved and are phylogenetically
+ limited. We have experimentally verified the efficiency and success of this
+ program. UniPrime is an experimentally validated, fully automated program that
+ generates successful cross-species primers that take into account the
+ biological aspects of the PCR.
+
+Depends: genetrack
+Homepage: http://sysbio.bx.psu.edu/genetrack.html
+License: MIT
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: genomic data storage and visualization framework
+ GeneTrack is a high performance bioinformatics data storage and analysis
+ system designed to store genome wide information. It is currently used to
+ analyze data obtained via high-throughput rapid sequencing platforms such as
+ the 454 and Solexa as well as tiling array data based on various platforms.
+
+Depends: operondb
+Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
+License: to be clarified
+Pkg-Description: detect and analyze conserved gene pairs
+ Comparison of complete microbial genomes reveals a large number of
+ conserved gene clusters - sets of genes that have the same order in
+ two or more different genomes. Such gene clusters often, but not
+ always represent a co-transcribed unit, or operon. A method was
+ developed to detect and analyze conserved gene pairs - pairs of genes
+ that are located close on the same DNA strand in two or more
+ bacterial genomes. For each conserved gene pair, an estimate of
+ probability is calculated that the genes belong to the same
+ operon. The algorithm takes into account several alternative
+ possibilities. One is that functionally unrelated genes may have the
+ same order due simply because they were adjacent in a common
+ ancestor. Other possibilities are that genes may be adjacent in two
+ genomes by chance alone, or due to horizontal transfer of the gene
+ pair.
+ .
+ The method is modified from the one described in: Maria D. Ermolaeva,
+ Owen White and Steven L. Salzberg. Prediction of Operons in Microbial
+ Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
+ .
+ OperonDB was supported by the NIH under grant R01-LM007938 and by the
+ NSF under grant DBI-0234704.
+Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
+ no info about license or downloadable code found, but tried to
+ contact authors.
+
+Depends: trnascan-se
+Homepage: http://lowelab.ucsc.edu/tRNAscan-SE/
+License: GPL
+Pkg-URL: http://bioweb.ucr.edu/debian-local/pool/main/t/trnascan-se/
+X-Category: tRNA discovery
+Pkg-Description: program for improved detection of transfer RNA genes in genomic sequence
+ tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence
+ while giving less than one false positive per 15 gigabases. Two
+ previously described tRNA detection programs are used as fast,
+ first-pass prefilters to identify candidate tRNAs, which are then
+ analyzed by a highly selective tRNA covariance model. This work
+ represents a practical application of RNA covariance models, which
+ are general, probabilistic secondary structure profiles based on
+ stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000
+ bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA
+ homologues such as selenocysteine tRNAs, tRNA-derived repetitive
+ elements and tRNA pseudogenes.
+
+Depends: beast-mcmc
+Homepage: http://beast.bio.ed.ac.uk/
+License: LGPL
+WNPP: 552101
+Responsible: Felix Feyertag <felix.feyertag at gmail.com>
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/beast-mcmc/trunk/
+Pkg-Description: Bayesian MCMC analysis of molecular sequences
+ BEAST is a cross-platform program for Bayesian MCMC analysis of
+ molecular sequences.  It is entirely orientated towards rooted,
+ time-measured phylogenies inferred using strict or relaxed molecular
+ clock models. It can be used as a method of reconstructing
+ phylogenies but is also a framework for testing evolutionary
+ hypotheses without conditioning on a single tree topology. BEAST uses
+ MCMC to average over tree space, so that each tree is weighted
+ proportional to its posterior probability. We include a simple to use
+ user-interface program for setting up standard analyses and a suit of
+ programs for analysing the results.
+ .
+ The source is avialable at http://code.google.com/p/beast-mcmc/ .
+Remark: Name space pollution
+ There is a Debian package beast which is completely unrelated
+ to this project.
+Published-Title: BEAST: Bayesian evolutionary analysis by sampling trees
+Published-Authors: A. J. Drummond, A. Rambaut
+Published-In: BMC Evolutionary Biology
+Published-Year: 2007
+Published-URL: http://www.biomedcentral.com/1471-2148/7/214/abstract
+Published-DOI: 10.1186/1471-2148-7-214
+Published-PubMed: 17996036
+
+Depends: artemis
+Homepage: http://www.sanger.ac.uk/Software/Artemis/
+License: GPL 2+
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: genome viewer and annotation tool
+ Artemis is a free genome viewer and annotation tool that allows visualization
+ of sequence features and the results of analyses within the context of the
+ sequence, and its six-frame translation. Artemis is written in Java, and is
+ available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK
+ database entries or sequence in FASTA or raw format. Extra sequence features
+ can be in EMBL, GENBANK or GFF format.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: act
+Homepage: http://www.sanger.ac.uk/Software/ACT/
+License: GPL
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-Description: DNA Sequence Comparison Viewer
+ ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer
+ based on Artemis. In common with Artemis, ACT is written in Java and
+ runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can
+ read complete EMBL and GENBANK entries or sequence in FASTA or raw
+ format. Extra sequence features can be in EMBL, GENBANK or GFF
+ format.
+ .
+ The sequence comparison displayed by ACT is usually the result of
+ running a blastn or tblastx search. See the user manual for more
+ information.
+ .
+ To see ACT in action go to the examples page
+ http://www.sanger.ac.uk/Software/ACT/Examples/
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Comment: If you stumble upon alfresco at
+ http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and
+ tarball vanished from the downlowad page.  So this is not for us even
+ if it is linked from Sanger Institute web site.
+
+Comment: If you stumble upon angler at
+ http://www.sanger.ac.uk/Software/Angler/ - it seems outdated because
+ it is not updated since 1997.  I found no license statement and so
+ this is probably also not for us except somebody has real interest
+ and volunteers to clarify the license.
+
+Depends: cdna-db
+Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
+License: Artistic
+Pkg-Description: quality-control checking of finished cDNA clone sequences
+ cdna_db is a software system designed for quality-control checking of
+ finished cDNA clone sequences, and their computational analysis. The
+ combination of a relational db (MySQL) schema, and an
+ object-orientated perl API make it easy to implement high-level
+ analyses of these transcript sequences.
+ .
+ The cdna_db can store cDNA clone sequences, and ESTs and
+ consensus/contig sequences also derived from these clones. These are
+ then used by the system to check cDNA clone sequence identity etc
+ (see deneral_doc.txt). For each clone multiple DNA sequence versions
+ can be stored, if for instance, the finished DNA sequence is revised
+ as part of the sequencing process.
+ .
+ A blast pipeline is implemented together with a job control system
+ (with LSF underlying) so that multiple CPUs can be used in parallel
+ to carry out the blasts of large datasets. The searches can be made
+ incremental, so as more cDNA sequences are added to the databank,
+ just the new clones are blasted.
+ .
+ Utility scripts are provided to delete previous search results, and
+ dump cDNA clones sequences (such as those that passed the QC
+ checking) from the cdna_db.
+
+Depends: das-proserver
+Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
+License: Same as Perl
+Pkg-Description: lightweight Distributed Annotation System (DAS) server
+ The Distributed Annotation System (DAS) is a data exchange protocol
+ for open sharing of biological information.
+ .
+ ProServer is a very lightweight DAS server written in Perl. It is
+ simple to install and configure and has existing adaptors for a wide
+ variety of data sources. It is also easily extensible allowing
+ adaptors to be written for other data sources. More information about
+ the DAS protocol and what it is useful for is available over at
+ http://biodas.org.
+ .
+ New large scale techniques in biology are producing a rapidly growing
+ amount of public available data. Centralized database resources are
+ confronted with the task how to scale their storage facilities, how
+ to manage frequent updates and how to exchange the data with the
+ community.
+ .
+ The Distributed Annotation System (DAS) addresses these issues. It is
+ frequently being used to openly exchange biological annotations
+ between distributed sites. Data distribution, performed by DAS
+ servers, is separated from visualization, which is done by DAS
+ clients.
+ .
+ DAS is a client-server system in which a client like Ensembl
+ integrates information from multiple servers. It allows a single
+ machine to gather up genome annotation information from multiple
+ distant web sites, collate the information, and display it to the
+ user in a single view. Little coordination is needed among the
+ various information providers.
+ .
+ DAS is heavily used in the genome bioinformatics community. Over the
+ last years we have also seen growing acceptance in the protein
+ sequence and structure communities.
+
+Depends: spice
+Homepage: http://www.efamily.org.uk/software/dasclients/spice/
+License: GPL
+Pkg-Description: Distributed Annotation System (DAS) client
+ The Distributed Annotation System (DAS) is a data exchange protocol
+ for open sharing of biological information.
+ .
+ SPICE is a browser for protein sequences, structures and their
+ annotations. It can display annotations for PDB, UniProt and Ensembl
+ Peptides. All data is retrieved from different sites on the Internet,
+ that make their annotations available using the DAS protocol. It is
+ possible to add new annotations to SPICE, and to compare them with
+ the already available information.
+
+Depends: decipher
+Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
+License: To be clarified
+Pkg-Description: tracks duplications and deletions of DNA in patients
+ DECIPHER tracks submicroscopic duplications and deletions of DNA in
+ patients together with phenotypes exhibited by those
+ patients. DECIPHER tallies these genetic abnormalities with genes and
+ other features of interest in the affected areas. The aim of DECIPHER
+ is to provide a research tool to aid clinical diagnosis and treatment
+ of these conditions. DECIPHER makes use of DAS technology to
+ integrate with Ensembl, the world's leading genome browser.
+
+Depends: est-db
+Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
+License: Artistic
+Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
+ The est_db package is a software suite and database system designed
+ to support expressed sequence tag (EST) sequencing projects, and to
+ provide comprehensive bioinformatic analysis of sequenced EST
+ libraries, for gene discovery and other purposes. The database can
+ hold and efficiently process hundreds of thousands of EST sequences,
+ track the cDNA libraries and clones to which they belong, and store
+ the results of their analysis. Should they be available, large
+ compute farms can be used for the analysis.
+ .
+ Extensive bioinformatic analysis can be carried out on the sequenced
+ EST libraries, including similarity (BLAST) searches, protein
+ sequence prediction, and the import of EST clustering and assembly
+ data from external sources. Results are searchable via a web page,
+ with graphic output of the various analyses, enabling one to retrieve
+ information pertaining to a particular cDNA clone, or EST read, as
+ well as view EST clustering results, or graphical representations of
+ BLAST results on the searched EST sequences.
+ .
+ The est_db package is likely to appeal not only to sequencing groups
+ directly employed in EST sequencing, but also to groups interested in
+ performing bespoke analysis of ESTs that may already be publically
+ available, in order to support their ongoing research aims. The
+ package is easily-extensible, via an API designed specifically to
+ handle ESTs and their analysis. It is open source and is made
+ available free of charge, and, where possible, similarly
+ open-licensed components have been used in its development.
+
+Depends: finex
+Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
+License: To be clarified
+Pkg-Description: sequence homology searching
+ The FINEX program allows sequence homology searching techniques to be
+ applied, where the sequence data is replaced with a fingerprint
+ abstracted from the intron/exon boundary phase and the exon length.
+ .
+ Please note FINEX is no longer supported but is available for
+ download.
+
+Depends: hexamer
+Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
+License: GPL
+Pkg-Description: scan DNA sequences to look for likely coding regions
+ Hexamer is a program to scan DNA sequences to look for likely coding
+ regions. The principle is to use 6mers, but to avoid deriving any
+ information from base composition. Therefore, the frequencies of each
+ 6mer are normalized by dividing by the total frequency of all 6mers
+ with the same base composition.
+ .
+ There are two programs involved in this process:
+  * hextable
+    hextable makes files of statistics that hexamer uses to scan for
+    likely coding regions.
+    The input of hextable is a fasta file of coding sequences in
+    frame.  The -o file output is an ascii list of 4096 floating point
+    numbers giving log likelihood ratio scores in bits.  The output on
+    stdout is a summary of the information content of the table,
+    indicating how disriminative it is likely to be.
+  * hexamer
+    Uses the .hex file from hextable to scan a DNA sequence for likely
+    coding regions.
+    The input is a fasta DNA file (n.b. that these programs assume all
+    'a','c','g','t'. 'n's found in the sequence files will be
+    converted to 'c'.
+    The output of hexamer is in General Feature Format (GFF) format.
+
+Depends: logomat-m
+Homepage: http://www.sanger.ac.uk/Software/analysis/logomat-m/
+License: As Perl itself
+Pkg-Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
+ Profile Hidden Markov Models (pHMMs) are a widely used tool for
+ protein family research. We present a method to visualize all of
+ their central aspects graphically, thus generalizing the concept of
+ sequence logos introduced by Schneider and Stephens. For each
+ emitting state of the pHMM, we display a stack of letters. As for
+ sequence logos, the stack height is determined by the deviation of
+ the position's letter emission frequencies from the background
+ frequencies of the letters. As a new feature, the stack width now
+ visualizes both the probability of reaching the state (the hitting
+ probability) and the expected number of letters the state emits
+ during a pass through the model (the expected contribution).
+ .
+ If you use HMM-Logos in your publication, please cite HMM Logos for
+ visualization of protein families.  Schuster-B"ockler B, Schultz J,
+ Rahmann S BMC Bioinformatics. 2004;5;7. PMID: 14736340 DOI:
+ 10.1186/1471-2105-5-7
+
+Depends: coot
+Homepage: http://www.ysbl.york.ac.uk/~emsley/coot/
+License: GPL
+Pkg-Description: protein structure model-building, -completion, -validation
+ The Crystallographic Object-Oriented Toolkit (Coot) displays maps and
+ models and allows model manipulations such as idealization, real space
+ refinement, manual rotation/translation, rigid-body fitting, ligand
+ search, solvation, mutations, rotamers, Ramachandran plots...
+
+Depends: r-ape
+Homepage: http://ape.mpl.ird.fr/
+License: GPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Analyses of Phylogenetics and Evolution
+ APE (Analyses of Phylogenetics and Evolution) is a package written in R.
+ APE aims to be both a computing tool to analyse phylogenetic and
+ evolutionary data, and an environment to develop and implement new
+ analytical methods.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: caftools
+Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
+License: Free for non-commercial purposes
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Tools to maintain DNA sequence assemblies
+ This is V2 of the CAF (Common Assembly Format) C-tools.  It comprises
+ a set of libraries and programs for manipulating DNA sequence
+ assemblies using CAF files.
+ .
+ The CAF specification can be found at:
+ http://www.sanger.ac.uk/Software/formats/CAF/
+Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
+ maintains a package called bio-linux-assembly-conversion-tools which
+ contains caftools and roche2gap in one package with the following
+ description:
+ .
+ Conversion tools for handling 454 assemblies.
+ .
+ This package contains code from different authors that allow sequence
+ assemblies to be converted into formats such as CAF (Common Assembly
+ Format) or GAP4. This package includes tools to convert assemblies
+ from Newbler's ace format for loading into a gap4 assembly.
+
+Depends: roche454ace2caf
+Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
+License: not specified
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: convert GS20 or FLX assemblies into CAF format
+ Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into
+ CAF format so that these are correct viewable/editable/... whithin
+ the staden package (gap4).  You have then access to "hidden data",
+ exact aligned trace and there positions, base values etc and whith
+ staden-1-7-0 you have graphical access to the associated flowgramm
+ traces (SFF format).
+ .
+ Description, Goals - please take a look at
+ http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf
+Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
+ maintains a package called bio-linux-assembly-conversion-tools which
+ contains caftools and roche2gap in one package with the following
+ description:
+ .
+ Conversion tools for handling 454 assemblies.
+ .
+ This package contains code from different authors that allow sequence
+ assemblies to be converted into formats such as CAF (Common Assembly
+ Format) or GAP4. This package includes tools to convert assemblies
+ from Newbler's ace format for loading into a gap4 assembly.
+
+Depends: big-blast
+Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Helper tool to run blast on large sequences
+ This script will chop up a large sequence, run blast on each bit and
+ then write out an EMBL feature table and a MSPcrunch -d file
+ containing the hits.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: blixem
+Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html
+License: not specified
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: interactive browser of pairwise Blast matches
+ Blixem (BLast matches In an X-windows Embedded Multiple alignment),
+ is an interactive browser of pairwise Blast matches that have been
+ stacked up in a ma ster-slave multiple alignment
+Remark: The link to the source archive on the web pages is not valid any more - it might be a problem to obtain the source.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: cap3
+Homepage: http://genome.cs.mtu.edu/cap/cap3.html
+License: free for governmental agency or a non-profit educational institution
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+X-Category: Sequence assembly
+X-Importance: not a lot of alternatives
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: DNA Sequence Assembly Program
+ CAP3 contains the following improvements to the CAP sequence assembly
+ program.
+  1. Use of forward-reverse constraints to correct assembly errors and
+     link contigs.
+  2. Use of base quality values in alignment of sequence reads.
+  3. Automatic clipping of 5' and 3' poor regions of reads.
+  4. Generation of assembly results in ace file format for Consed.
+  5. CAP3 can be used in GAP4 of the Staden package.
+ These improvements allow CAP3 to take longer sequences of higher
+ errors and produce more accurate consensus sequences.
+Remark: Obtaining the source requires to fill in a registration form
+ Official distribution in Debian is probably impossible.  The
+ package included in the BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html containins only the binaries
+ cap3 and formcon, dated Aug 29, 2002.  This package exists purely for
+ convenience to Bio-Linux users so that the files are placed in
+ locations consistent with the Bio-Linux setup.
+
+Depends: cd-hit
+Homepage: http://www.bioinformatics.org/cd-hit/
+License: GPLv2
+WNPP: 652074
+Responsible: Andreas Tille <tille at debian.org>
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cd-hit/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cd-hit/trunk/
+Pkg-Description: suite of programs designed to quickly group sequences.
+ CD-HIT stands for Cluster Database at High Identity with
+ Tolerance. The program (cd-hit) takes a fasta format sequence
+ database as input and produces a set of 'non-redundant' (nr)
+ representative sequences as output. In addition cd-hit outputs a
+ cluster file, documenting the sequence 'groupies' for each nr
+ sequence representative. The idea is to reduce the overall size of
+ the database without removing any sequence information by only
+ removing 'redundant' (or highly similar) sequences. This is why the
+ resulting database is called non-redundant (nr). Essentially, cd-hit
+ produces a set of closely related protein families from a given fasta
+ sequence database.
+ .
+ CD-HIT uses a 'longest sequence first' list removal algorithm to
+ remove sequences above a certain identity threshold. Additionally the
+ algorithm implements a very fast heuristic to find high identity
+ segments between sequences, and so can avoid many costly full
+ alignments.
+ .
+ With recent developments, cd-hit package offers new programs for DNA
+ sequence clustering and comparing two databases. It also has lots of
+ new options for clustering control.
+
+Comment: BioLinux contains a clcworkbench package which is available
+ at http://www.clcbio.com/index.php?id=28 but this seems to be only
+ "free as in beer" binary download - so this is not for us ...
+
+Depends: coalesce
+Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: outdated program to estimate population-genetic parameters
+ COALESCE fits the model which has a single population of constant
+ size, and estimates 4Nu, where N is the effective population size and
+ u is the neutral mutation rate per site. You may also want the
+ Postscript or the TeX file of the preprint version of the Kuhner,
+ Yamato, and Felsenstein 1995 paper.
+Remark: This software is probably outdated
+ The homepage contains the explicite link: "We are no longer
+ supporting COALESCE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however."  So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Comment: BioLinux contains a dendroscope package which is available
+ at http://www.dendroscope.org but this project has only a
+ "free as in beer" binary download - so this is not for us ...
+
+Depends: estferret
+Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
+License: to be clarified
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: processes, clusters and annotates EST data
+ ESTFerret processes, clusters and annotates EST data. It is
+ user-configurable. Results are currently stored in a series of text
+ tables. Annotation consists of searches against use r-defined blast
+ databases, prosite, GO and allocation of EC numbers where possible.
+ .
+ EST-ferret is a user-configurable, automated pipeline for the
+ convenient analysis of EST sequence data that includes all of the
+ necessary steps for cleanup and trimming, submission to external
+ sequence repositories, clustering, identification by BLAST homology
+ searches and by searches of protein domain databases, annotation with
+ computer-addressable terms and production of outputs for direct entry
+ into microarray analysis packages. It is composed of several widely
+ used, open-source algorithms, including PHRED, CAP3, BLAST, and a
+ range of sequence and annotation databases, including Gene Ontology
+ and Conserved Domain Database to deliver a putative identity and a
+ detailed annotation of each clone. It can be run either step-by-step
+ to track the outputs, or as a single batch process. Users can easily
+ edit the configuration file to define parameter settings.
+ .
+ This package has five major components: (1) ESTs coding system; (2)
+ sequence processing; (3) sequence clustering; (4) sequence annotating
+ and (5) storage and reporting of results. DNA trace files are renamed
+ and converted into FASTA format, cleaned and submitted to
+ dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of
+ CAP3 to assemble the ESTs into groups corresponding to separate gene
+ families and unique genes. Sequence identification and annotation is
+ provided by a series of BLAST homology searches (Parallel_BLAST and
+ Priority_BLAST) against user-defined sequence databases implemented
+ with the NCBI BLASTALL algorithm. The BLAST results are parsed and
+ annotation terms that reflect functional attributes are captured from
+ Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme
+ Commission (EC) databases and applied to each of the clones. CDD (and
+ InterPro) searches are performed for seeking protein domains in the
+ sequences. Other options are provided to run PatSearch, RepeatMasker
+ and BLAT to find UTRs, repeats and EST candidates in
+ genomes. Finally, the package generates analysis reports in a variety
+ of flat file formats, sources of which can be serve as inputs for
+ some gene annotation and gene expression profiling tools, and also as
+ a MySQL database or web-browsable search tool.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: estscan
+Homepage: http://estscan.sourceforge.net/
+License: free
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detect coding regions in DNA sequences, even if of low quality
+ ESTScan is a program that can detect coding regions in DNA sequences,
+ even if they are of low quality. It will also detect and correct
+ sequencing errors that lead to fr ameshifts.
+ .
+ ESTScan is not a gene prediction program, nor is it an open reading
+ frame detector. In fact, its strength lies in the fact that it does
+ not require an open reading frame to detect a coding region. As a
+ result, the program may miss a few translated amino acids at either
+ the N or the C terminus, but will detect coding regions with high
+ selectivity and sensitivity.
+ .
+ Similarly to GENSCAN, ESTScan uses a Markov model to represent the
+ bias in hexanucleotide usage found in coding regions relative to
+ non-coding regions. Additionally, ESTScan allows insertions and
+ deletions when these improve the coding region statistics. Further
+ details can be found at:
+ http://www.ch.embnet.org/software/ESTScan2_help.html
+ .
+ References:
+  * Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing
+    errors by combining Hidden Markov models Bioinformatics 19,
+    ii103-ii112.
+  * Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for
+    detecting, evaluating, and reconstructing potential coding regions in
+    EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: fasta
+Homepage: http://www.ebi.ac.uk/Tools/fasta/
+License: no inclusion into commercial product
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: searching DNA and protein databases
+ FASTA (pronounced FAST-AYE) stands for FAST-ALL, reflecting the fact
+ that it can be used for a fast protein comparison or a fast
+ nucleotide comparison. This program achieves a high level of
+ sensitivity for similarity searching at high speed. This is achieved
+ by performing optimised searches for local alignments using a
+ substitution matrix. The high speed of this program is achieved by
+ using the observed pattern of word hits to identify potential matches
+ before attempting the more time consuming optimised search. The
+ trade-off between speed and sensitivity is controlled by the ktup
+ parameter, which specifies the size of the word. Increasing the ktup
+ decreases the number of background hits. Not every word hit is
+ investigated but instead initially looks for segment's containing
+ several nearby hits.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: fluctuate
+Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: outdated program to model a single population
+ FLUCTUATE fits the model which has a single population which has been
+ growing (or shrinking) according to an exponential growth law. It
+ estimates 4Nu and g, where N is the effective population size, u is
+ the neutral mutation rate per site, and g is the growth rate of the
+ population.
+Remark: This software is probably outdated
+ The homepage contains the explicite link: "We are no longer
+ supporting FLUCTUATE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however."  So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Depends: forester
+Homepage: http://sourceforge.net/projects/forester-atv/
+License: LGPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: visualization of annotated phylogenetic trees
+ FORESTER is a Java/Perl based software package for phylogenomic
+ analyses. Currently, it includes the phylogenetic tree visualization
+ and manipulation tool ATV and implementations of the SDI algorithm
+ and the RIO method (http://www.phylosoft.org/).
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: jalview
+Homepage: http://www.jalview.org/
+License: GPL
+WNPP: 507436
+Responsible: Vincent Fourmond <fourmond at debian.org>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: multiple alignment editor
+ Jalview is a multiple alignment editor written in Java. It is used
+ widely in a variety of web pages (e.g. the EBI Clustalw server and
+ the Pfam protein domain database) but is available as a general
+ purpose alignment editor.
+
+Depends: lamarc
+Homepage: http://evolution.gs.washington.edu/lamarc/
+License: Apache V2.0
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: estimate population-genetic parameters
+ LAMARC is a program which estimates population-genetic parameters
+ such as population size, population growth rate, recombination rate,
+ and migration rates. It approximates a summation over all possible
+ genealogies that could explain the observed sample, which may be
+ sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
+ its sister program Migrate are successor programs to the older
+ programs Coalesce, Fluctuate, and Recombine, which are no longer
+ being supported. The programs are memory-intensive but can run
+ effectively on workstations.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: lucy
+Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: DNA sequence quality and vector trimming tool
+ Lucy is a utility that prepares raw DNA sequence fragments for
+ sequence assembly, possibly using the TIGR Assembler. The cleanup
+ process includes quality assessment, confidence reassurance, vector
+ trimming and vector removal. The primary advantage of Lucy over other
+ similar utilities is that it is a fully integrated, stand alone
+ program.
+ .
+ Lucy was designed and written at The Institute for Genomic Research
+ (TIGR, now the J. Craig Venter Institute), and it has been used here
+ for several years to clean sequence data from automated DNA
+ sequencers prior to sequence assembly and other downstream uses.  The
+ quality trimming portion of lucy makes use of phred quality scores,
+ such as those produced by many automated sequencers based on the
+ Sanger sequencing method.  As such, lucy’s quality trimming may not
+ be appropriate for sequence data produced by some of the new
+ “next-generation” sequencers.
+ .
+ See also the SourceForge page at http://lucy.sourceforge.net/.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: maxd
+Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
+License: Artistic
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: data warehouse and visualisation environment for genomic expression data
+ Maxd is a data warehouse and visualisation environment for genomic
+ expression data. It is being developed in the University of
+ Manchester by the Microarray Bioinformatics Group.
+ .
+ Software components:
+  maxdLoad2 - standards-compliant, highly customisable transcriptomics
+              database
+  maxdView  - modular and easily extensible data visualisation and
+              analysis environment
+  maxdSetup - installation management utility
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: mesquite
+Homepage: http://mesquiteproject.org/mesquite/mesquite.html
+License: LGPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: help biologists analyze comparative data about organisms
+ Mesquite is software for evolutionary biology, designed to help
+ biologists analyze comparative data about organisms. Its emphasis is
+ on phylogenetic analysis, but some of its modules concern population
+ genetics, while others do non-phylogenetic multivariate
+ analysis. Because it is modular, the analyses available depend on the
+ modules installed. Analyses include:
+  * Reconstruction of ancestral states (parsimony, likelihood)
+  * Tests of process of character evolution, including correlation
+  * Analysis of speciation and extinction rates
+  * Simulation of character evolution (categorical, DNA, continuous)
+  * Parametric bootstrapping (integration with programs such as PAUP*
+    and NONA)
+  * Morphometrics (PCA, CVA, geometric morphometrics)
+  * Coalescence (simulations, other calculations)
+  * Tree comparisons and simulations (tree similarity, Markov
+    speciation models)
+ There is a brief outline of features, which includes
+ screenshots. Mesquite is not primarily designed to infer phylogenetic
+ trees, but rather for diverse analyses using already inferred trees.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: migrate
+Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
+License: to be clarified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: estimation of population sizes and gene flow using the coalescent
+ Migrate estimates effective population sizes and past migration rates
+ between n population assuming a migration matrix model with
+ asymmetric migration rates and different subpopulation sizes. Migrate
+ uses maximum likelihood or Bayesian inference to jointly estimate all
+ parameters. It can use the followind data types: sequence data using
+ Felsenstein's 84 model with or without site rate variation, single
+ nucleotide polymorphism data, microsatellite data using a stepwise
+ mutation model or a brownian motion mutation model, and
+ electrophoretic data using an 'infinite' allele model. The output can
+ contain: Estimates of all migration rates and all population sizes,
+ assuming constant mutation rates among loci or a gamma distributed
+ mutation rate among loci. Profile likelihood tables, Percentiles,
+ Likelihood-ratio tests, and simple plots of the log-likelihood
+ surfaces for all populations and all loci.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: msatfinder
+Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
+License: GPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: identification and characterization of microsatellites in a comparative genomic context
+ Msatfinder is a Perl script designed to allow the identification and
+ characterization of microsatellites in a comparative genomic
+ context. There is also an online manual, a discussion forum and an
+ online interface where users can do searches in any number of DNA or
+ protein sequences (as long as the maximum size of all sequences does
+ not exceed 10MB). Nucleotide and amino acid sequences in GenBank,
+ FASTA, EMBL and Swissprot formats are supported.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: mview
+Homepage: http://bio-mview.sourceforge.net/
+License: GPL
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: reformat results of a sequence database search or a multiple alignment
+ MView is a tool for converting the results of a sequence database
+ search (BLAST, FASTA, etc.) into the form of a coloured multiple
+ alignment of hits stacked against the query. Alternatively, an
+ existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be pr
+ ocessed.  It reformats the results of a sequence database search or a
+ multiple alignment adding optional HTML markup to control colouring
+ and web page layout. MView is not a multiple alignment program, nor
+ is it a general purpose alignment editor.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: oligoarrayaux
+Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
+License: non-free (fre academical use)
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Prediction of Melting Profiles for Nucleic Acids
+ OligoArrayAux is a subset of the UNAFold package for use with
+ OligoArray (http://berry.engin.umich.edu/oligoarray2_1/). OligoArray
+ is a free software that computes gene specific oligonucleotides for
+ genome-scale oligonucleotide microarray construction.  (It is not
+ really specified what they mean with "free software". You can
+ download the source code after registration: "registration is the
+ only way for me to keep trace of OligoArray users and be able to send
+ you a bug fix or a new release".)
+ .
+ The original UNAFold server is available at
+ http://dinamelt.bioinfo.rpi.edu/download.php and you should probably
+ read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about
+ "Prediction of Melting Profiles for Nucleic Acids".
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+ Finally it is hard to find some documentation what OligoArrayAux is
+ really doing because it is only specified into relation to OligoArray
+ (as precondition) and UNAFold (as subset of this) but BioLinux
+ distribution http://envgen.nox.ac.uk/biolinux.html decided to package
+ this and so it might make soem sense to list it here - further
+ investigation is needed.
+
+Depends: omegamap
+Homepage: http://www.danielwilson.me.uk/software.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: detecting natural selection and recombination in DNA or RNA sequences
+ OmegaMap is a program for detecting natural selection and
+ recombination in DNA or RNA sequences. It is based on a model of
+ population genetics and molecular evolution. The signature of natural
+ selection is detected using the dN/dS ratio (which measures the
+ relative excess of non-synonymous to synonymous polymorphism) and the
+ signature of recombination is detected from the patterns of linkage
+ disequilibrium. The model and the method of estimation are described
+ in
+  Wilson, D. J. and G. McVean (2006)
+  Estimating diversifying selection and functional constraint in the
+  presence of recombination.
+  Genetics doi:10.1534/genetics.105.044917.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: partigene
+Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: generating partial gemomes
+ PartiGene is part of the Edinburgh-EGTDC developed EST-software
+ pipeline at the moment consisting of trace2dbEST, PartiGene,
+ wwwPartiGene, port4EST and annot8r. PartiGene is a menu-driven,
+ multi-step software tool which takes sequences (usually ESTs) and
+ creates a dataabase of a non-redundant set of sequence objects
+ (putative genes) which we term a partial genome.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: pfaat
+Homepage: http://pfaat.sourceforge.net/
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Protein Family Alignment Annotation Tool
+ Pfaat is a Java application that allows one to edit, analyze, and
+ annotate multiple sequence alignments. The annotation features are a
+ key component as they provide a framework to for further sequence,
+ structure and statistical analysis.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: pftools
+Homepage: http://www.isrec.isb-sib.ch/profile/profile.html
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: handle profiles of protein domains
+ The 'pftools' package is a collection of experimental programs
+ supporting the generalized profile format and search method of
+ PROSITE.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: prank
+Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
+License: GPL (except two algorithms)
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Enhances: t-coffee
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
+ PRANK is a probabilistic multiple alignment program for DNA, codon
+ and amino-acid sequences. It's based on a novel algorithm that treats
+ insertions correctly and avoids over-estimation of the number of
+ deletion events. In addition, PRANK borrows ideas from maximum
+ likelihood methods used in phylogenetics and correctly takes into
+ account the evolutionary distances between sequences. Lastly, PRANK
+ allows for defining a potential structure for sequences to be aligned
+ and then, simultaneously with the alignment, predicts the locations
+ of structural units in the sequences.
+ .
+ PRANK is a command-line program for Unix-style environments but the
+ same sequence alignment engine is implemented in the graphical
+ program PRANKSTER. In addition to providing a user-friendly interface
+ to those not familiar with Unix systems, PRANKSTER is an alignment
+ browser for alignments saved in the HSAML format. The novel format
+ allows for storing all the information generated by the aligner and
+ the alignment browser is a convenient way to analyse and manipulate
+ the data.
+ .
+ PRANK aims at an evolutionarily correct sequence alignment and often
+ the result looks different from ones generated with other alignment
+ methods. There are, however, cases where the different look is caused
+ by violations of the method's assumptions. To understand why things
+ may go wrong and how to avoid that, read this explanation of
+ differences between PRANK and traditional progressive alignment
+ methods.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+ Precondition for T-Coffee (see http://wiki.debian.org/DebianMed/TCoffee)
+
+Comment: priam
+ BioLinux contains a priam package which is available at
+ http://bioinfo.genotoul.fr/priam/REL_JUL06/index_jul06.html but this
+ project has only a "free as in beer" binary download - so this is not
+ for us ...
+
+Depends: prot4est
+Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: EST protein translation suite
+ prot4EST is a perl script that takes expressed sequence tags (ESTs)
+ and translates them optimally to produce putative peptides. prot4EST
+ intergrates a number of programs to overcome problems inherent with
+ translating ESTs.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: qtlcart
+Homepage: http://statgen.ncsu.edu/qtlcart/
+License: GPL
+Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: map quantitative traits using a map of molecular markers
+ QTL Cartographer is a suite of programs to map quantitative traits
+ using a map of molecular markers. It contains a set of programs that
+ will aid in locating the genes that control quantitative traits using
+ a molecular map of markers.  It includes some programs to allow
+ simulation studies of experiments.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: rbs-finder
+Homepage: http://www.genomics.jhu.edu/RBSfinder/
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: find ribosome binding sites(RBS)
+ The program implements an algorithm to find ribosome binding
+ sites(RBS) in the upstream regions of the genes annotated by
+ Glimmer2, GeneMark, or other prokaryotic gene finders.  If there is
+ no RBS-like patterns in this region, program searches for a start
+ codon having a RBS-like pattern ,in the same reading frame upstream
+ or downstream and relocates start codon accordingly.
+ .
+ You can find more detailed information at
+ http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: recombine
+Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: effective population size of populations
+ RECOMBINE fits a model which has a single population of constant size
+ with a single recombination rate across all sites. It can accomodate
+ either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism)
+ data. It estimates 4Nu and r, where N is the effective population
+ size, u is the neutral mutation rate per site, and r is the ratio of
+ the per-site recombination rate to the per-site mutation rate.
+Remark: This software might be outdated
+ The homepage contains the explicite link: "We are no longer
+ supporting RECOMBINE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however."  So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.
+
+Depends: splitstree
+Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
+License: to be clarified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Analyzing and Visualizing Evolutionary Data
+ Evolutionary data is most often presented as a phylogentic tree, the
+ underlying assumption being that evolution is a branching
+ process. However, real data is never ideal and thus doesn't always
+ support a unique tree, but often supports more than one possible
+ tree. Hence, it makes sense to consider tree reconstruction methods
+ that produce a tree, if the given data heavily favors one tree over
+ all others, but otherwise produces a more general graph that
+ indicates different possible phylogenies. One such method is the
+ Split Decomposition introduced by Hans-Juergen Bandelt and Andreas
+ Dress (1992) and its variations. Another example is Spectral Analysis
+ developed by Hendy, Penny and others.
+ .
+ These and other methods are implemented in the program SplitsTree,
+ that I wrote with contributions from Dave Bryant, Mike Hendy, Holger
+ Paschke, Dave Penny and Udo Toenges. It is based on the Nexus
+ format.
+ .
+ Note: There is a new version 4.0 written from scratch at
+ http://www.splitstree.org/ which requires a license key - so this is
+ probably non-free.  Version 3.2 which is linked above has some
+ downloadable source code without any license or copyright statement -
+ so it has to be clarified whether we are able to distribute this code
+ or not.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+
+Depends: taverna
+Homepage: http://taverna.sourceforge.net/
+License: LGPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: designing and executing myGrid workflows for bioinformatics
+ The Taverna workbench is a free software tool for designing and
+ executing workflows, created by the myGrid  project, and funded
+ through OMII-UK. Taverna allows users to integrate many different
+ software tools, including web services, such as those provided by the
+ National Center for Biotechnology Information, The European
+ Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab,
+ BioMOBY and EMBOSS.
+ .
+ The Taverna Workbench provides a desktop authoring environment and
+ enactment engine for scientific workflows expressed in Scufl (Simple
+ Conceptual Unified Flow language). The Taverna enactment engine is
+ also available separately, and other Scufl enactors are available
+ including Moteur. The myExperiment social web site supports finding
+ and sharing of workflows and has special support for Scufl
+ workflows. The Taverna workbench, myExperiment and associated
+ components are developed and maintained by the myGrid team, in
+ collaboration with the open source community.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: taxinspector
+Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
+License: Artistic + other free licenses
+Responsible: BioLinux - Tim Booth <tbooth at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: browser for entries in the NCBI taxonomy
+ TaxInspector is a browser for entries in the NCBI taxonomy. It is
+ designed to run as a plugin to annotation software such as maxdLoad2
+ and Pedro, but also has a standalone mode.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: tetra
+Homepage: http://www.megx.net/tetra/
+License: free academic
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: tetranucleotide frequency calculator
+ The TETRA program can be used to calculate how well tetranucleotide
+ usage patterns in DNA sequences correlate. Such correlations can
+ provide valuable hints on the relatedne ss of DNA sequences, and are
+ particularly useful for metagenomic sequences.
+Remark: for the Linux version
+ Version 1.0.2 (Mac OSX has version
+ 2.0b30) is deprecated and hence a feature-limited version of
+ TETRA. At the time writing, no decisions have been made about
+ adapting and cross-compiling the Mac OS X code for this platform. A
+ Linux version might happen when REALbasic's Linux IDE is more mature.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: trace2dbest
+Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
+License: GPL
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: process trace files into dbEST submissions
+ Trace2dbest is part of the PartiGene pipeline.
+ .
+ Trace2dbest takes a series of sequence traces and converts them into
+ basecalled files. It also creates files in the appropriate format for
+ submission to dbEST and allows you to submit them directly if your
+ machine is configured to allow mailing to external sites.  The output
+ from trace2dbest can be used as input to the PartiGene program.
+ .
+ Trace2dbEST process raw sequenceing chromatograph trace files from
+ EST projects into quality-checked sequences, ready for submission to
+ dbEST. trace2dbEST guides you through the creation of all the
+ necessary files for submission of ESTs to dbEST. trace2dbest makes
+ use of other software (available free under academic licence) that
+ you will need to have installed, namely phred, cross_match and
+ (optionaly) BLAST.
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+Depends: profit
+Homepage: http://www.bioinf.org.uk/software/profit/
+License: non-free
+Responsible: Steffen Moeller <steffen_moeller at gmx.de>
+WNPP: 525428
+Pkg-Description: structural alignment of multiple proteins
+ ProFit is designed to be the ultimate protein least squares fitting
+ program. It has many features including flexible specification of
+ fitting zones and atoms, calculation of RMS over different zones or
+ atoms, RMS-by-residue calculation, on-line help facility, etc.
+Remark: The authors need to change the license, still.
+ The debian folder should appear in Debian Med Svn in some near future.
+
+Depends: kempbasu
+Homepage: http://code.google.com/p/kempbasu/
+License: GPL
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/kempbasu/trunk/
+Responsible: Charles Plessy <plessy at debian.org>
+Pkg-Description: Significance tests for comparing digital gene expression profiles
+ This package implements the significance tests for comparing digital
+ gene profiles described in the article:
+ .
+ Varuzza _et al_. *"Significance tests for comparing digital gene
+ expression profiles"*
+ .
+ They provide two programs: kemp for the frequentist test and basu for
+ the Bayesian test, and some auxiliary scripts.
+
+Depends: grogui
+Homepage: http://www.kde-apps.org/content/show.php?content=47665
+License: GPL
+Pkg-Description: graphical user interface for popular molecular dynamics package GROMACS
+  1. File browsing and management with customizable right-click pop up menu.
+  2. Graphical interfaces for GROMACS commands (currently 21 commands have their own interfaces).
+  3. Plot drawing tool which can export plots to pdf.
+  4. A simple built-in console.
+  5. Built-in GROMACS manual viewer.
+  6. Built-in file editor with syntax highlighting for some GROMACS file formats (currently only mdp format is supported).
+  7. MDP Writer section to easily create your mdp files.
+  8. File icons based on their types.
+
+Depends: rosetta
+Homepage: http://www.rosettacommons.org/
+License: not redistributable, not unlikely to change
+Pkg-Description: Protein-folding, -docking, ..?
+ Rosetta is a much renowned tool for the molecular modelling of protein
+ structures, small chemicals, and interactions between any of these.
+ It is developed by a consortium of several american academic research
+ groups. Industry can buy licenses from a not-for-profit company, while
+ academic groups have the opportunity to download the source and build
+ it locally. That license explicitly denies the right to redistribute
+ the source or binaries. Nevertheless, Debian Med could possibly offer
+ an easy preparation of Debian packages.
+
+Depends: obo-edit
+Homepage: http://www.geneontology.org
+License: something free
+Pkg-Description: editor for biological ontologies
+ (Open Biological Ontologies) Obo-Edit supports the formal representation
+ of biological entities and the specification of is-a (specialisation)
+ and part-of relations. Amongst the databases cureated by this tool
+ is the GeneOntology.
+
+Depends: lagan
+Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
+License: GPL
+Pkg-Description: highly parametrizable pairwise global alignment program
+ Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of
+ the Needleman-Wunsch algorithm around these anchors.
+ .
+ Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment.
+ M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic
+ tree. Alignments are aligned to other alignments using the sum-of-pairs metric.
+Remark: May be packaged in local repository
+ A local package is mentioned at
+ https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Local%20Debian%20Repository
+ but the package does not seem to be available publicly.  It might be a good idea to ask
+ there before starting packaging.
+Published-Title: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
+Published-Authors: Michael Brudno, Chuong Do, Gregory Cooper, Michael F. Kim, Eugene Davydov, Eric D. Green, Arend Sidow, Serafim Batzoglou
+Published-In: Genome Research 13(4):721-31.
+Published-Year: 2003
+Published-URL: http://lagan.stanford.edu/lagan_web/mlagan_gr.pdf
+X-Category: Comparative genomics
+
+Depends: jstreeview
+Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml
+License: MIT/X11
+Language: JavaScript
+Pkg-Description: Editor for Phylogenetic Trees
+ A concise viewer/editor for phylogenetic trees in the Newick format.
+ The core functions are written in JavaScript, using the canvas tag
+ proposed by HTML 5. No server side support is needed for rendering the
+ picture and therefore you can grab this page together with knhx.js and
+ canvastext.js to locally view your trees in a supported web browser.
+ .
+ The source can be downloaded at
+ http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip
+
+Depends: phagefinder
+Homepage: http://phage-finder.sourceforge.net/
+License: GPL
+Language: Perl
+X-Category: Genomics; Prophage detection in prokaryotes
+Pkg-Description: heuristic computer program to identify prophage regions within bacterial genomes
+ It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a
+ collection of bacteriophage protein sequences and results from HMMSEARCH analysis of
+ 441 phage-specific HMMs to locate prophage regions. By using FASTA33, MUMMER  or BLASTN,
+ it can find potential attachment (att) sites of the phage region(s). Data from tRNAscan-SE
+ and Aragorn  are used to determine whether a tRNA  or tmRNA  served as the putative target
+ for integration. Additionally, by looking for the presence or absence of specific proteins
+ using specific HMM models, Phage_Finder can predict whether the region is most likely
+ prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a
+ degenerate phage region.
+ .
+ The goal of this project is to provide an open-sourced, standardized and automated system
+ to identify and classify prophages within prokaryotic genomes. It is hoped that this package
+ will facilitate future studies on the biology and evolution of these prophages by providing
+ a level of microbial genome annotation that was previously void.
+
+Depends: codonw
+Homepage: http://codonw.sourceforge.net/
+License: GPL
+X-Category: Genomics; Codon usage analysis
+Pkg-Description: Correspondence Analysis of Codon Usage
+ CodonW is a programme designed to simplify the Multivariate analysis (correspondence
+ analysis) of codon and amino acid usage. It also calculates standard indices of codon
+ usage. It has both menu and command-line interfaces. It was written by John Peden in
+ the lab of Paul Sharp,  Dept of Genetics,  University of Nottingham. John is working
+ in human genetics and is currently employed as ProCardis database manager at the WTCHG
+ in Oxford University.
+
+Depends: compclust
+Homepage: http://woldlab.caltech.edu/compclust/
+License: MLX (http://woldlab.caltech.edu/compclust/LICENSE.txt)
+Language: Python
+X-Category: Genomics; Clustering analysis (+GUI)
+Pkg-URL: http://woldlab.caltech.edu/compclust/debian_install.shtml
+Pkg-Description: explore and quantify relationships between clustering results
+ CompClust is a python package written using the pyMLX and IPlot APIs. It provides
+ software tools to explore and quantify relationships between clustering results. Its
+ development has been largely built around needs of microarray data analysis but could
+ be easily used in other domains.
+ .
+ Briefly pyMLX provides for efficient and convenient execution of many clustering
+ algorithms using a extendable library of algorithms. It also provides many-to-many
+ linkages between data features and annotations (such as cluster labels, gene names,
+ gene ontology information, etc.) These linkages persist through varied data
+ manipulations. IPlot provides an abstraction of the plotting process in which any
+ arbitrary feature or derived feature of the data can be projected onto any feature
+ of the plot, including the X,Y coordinates of points, marker symbol, marker size,
+ maker/line color, etc. These plots are intrinsically linked to the dataset, the
+ View and the Labeling classes found within pyMLX.
+
+Depends: treebuilder3d
+Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder
+License: GPL
+Language: Java
+X-Category: Clustering; SAGE expression
+Pkg-Description: viewer of SAGE and other types of gene expression data
+ TreeBuilder3D is an interactive viewer that allows organization of SAGE and other
+ types of gene expression data such as microarrays into hierarchical dendrograms,
+ or phenetic networks (the term 'phenetic' used as the analysis relies on principals,
+ used in phylogenetic analysis by system biology). Might be used as a visual aid when
+ analyzing differences in expression profiles of SAGE libraries, serves as an
+ alternative to Venn diagrams.
+
+Depends: excavator
+Homepage: http://csbl.bmb.uga.edu/downloads/excavator/
+License: GPL
+Language: Java
+X-Category: Clustering; Gene expression data
+Pkg-Description: gene expression data clustering
+ Excavator is a program for gene expression data clustering. It uses a set of unique
+ clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at
+ the University of Georgia. Excavator represents data internally as a minimum spanning
+ tree and outputs results to the user through the use of a micro-array data window,
+ graphs, and a dendrogram viewer.
+ .
+ Features
+  * partitioning gene expressions profiles using multiple methods of clustering and
+    definitions of distance between profiles.
+  * automatic selection of the most plausible number of clusters in a data set
+  * three different ways of viewing data: Micro-array, Gene Expression, and Dendrogram.
+    As well as graphing individual genes from each cluster independently.
+  * identification of genes with expression profiles similar to specified seed genes
+  * cluster identification from a noisy background
+  * numerical comparison between different clustering results of the same data set
+  * runnable on command line as well as through a Java GUI
+
+Depends: tigr-assembler
+Homepage: http://www.jcvi.org/cms/research/software/
+License: free (OSI-certified)
+X-Category: Assembling
+Pkg-Description: whole-genome assembly
+ Enabled the first published whole-genome assembly of a free-living organism in 1995.
+ Last revised in 2003.
+ .
+ See also http://www.jcvi.org/cms/publications/listing/abstract/article/tigr-assembler-a-new-tool-for-assembling-large-shotgun-sequencing-projects/
+Remark: It seems that wgs-assembler is the more up to date program.  Moreover there
+ seems to be no download option for TIGR Assembler at the J. Craig Venter Institute
+ (formerly TIGR) any more.
+
+Depends: crossbow
+Homepage: http://bowtie-bio.sourceforge.net/crossbow
+License: Artistic
+X-Category: Sequencing
+Pkg-Description: Genotyping from short reads using cloud computing
+ Crossbow is a scalable software pipeline for whole genome resequencing
+ analysis. It combines Bowtie, an ultrafast and memory efficient short read
+ aligner, and SoapSNP, an accurate genotyper, within Hadoop to distribute and
+ accelerate the computation with many nodes. The pipeline can accurately analyze
+ over 35x coverage of a human genome in one day on a 10-node local cluster, or
+ in 3 hours for about $100 using a 40-node, 320-core cluster rented from
+ Amazon's EC2 utility computing service.
+Published-Title: Searching for SNPs with cloud computing
+Published-Authors: Ben Langmead, Michael Schatz, Jimmy Lin, Mihai Pop, Steven Salzberg
+Published-In: Genome Biology
+Published-Year: 2009
+Published-URL: http://genomebiology.com/2009/10/11/R134
+Published-DOI: 10.1186/gb-2009-10-11-r134
+
+Depends: cufflinks
+WNPP: 627799
+Homepage: http://cufflinks.cbcb.umd.edu/
+Vcs-Git: git://git.debian.org/debian-med/cufflinks.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
+License: Boost
+X-Category: Sequencing
+Pkg-Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq
+ Cufflinks assembles transcripts, estimates their abundances, and tests for
+ differential expression and regulation in RNA-Seq samples. It accepts aligned
+ RNA-Seq reads and assembles the alignments into a parsimonious set of
+ transcripts. Cufflinks then estimates the relative abundances of these
+ transcripts based on how many reads support each one.
+Published-Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
+Published-Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
+Published-In: Nature Biotechnology
+Published-DOI: doi:10.1038/nbt.1621
+Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
+Published-Year: 2010
+
+Depends: ncbi-blast+
+
+Depends: treetime
+Homepage: http://treetime.linhi.com/
+License: GPL
+Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data
+ TreeTime is controlled by input files in nexus format and does
+ bayesian sampling of phylogenetic trees from these data.
+
+Depends: biomaj
+
+Depends: abacas
+
+Depends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun
+X-Remark: The profnet homepage contains an image of a complete Debian system.  The Debian Med
+          team tries to support the authors by providing binary packages inside Debian.
+
+Depends: profphd-net, profphd-utils
+
+Depends: profphd
+Published-Title: Combining evolutionary information and neural networks to predict protein secondary structure.
+Published-Authors: Rost, B. and Sander, C.
+Published-In: Proteins. 19(1):55-72
+Published-Year: 1994
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/8066087
+Published-PubMed: 8066087
+
+Depends: abyss
+Published-Title: ABySS: A parallel assembler for short read sequence data
+Published-Authors: Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
+Published-In: Genome Research
+Published-Year: 2009
+
+Depends: ampliconnoise
+Published-Authors: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
+Published-Title: Removing Noise From Pyrosequenced Amplicons
+Published-In: BMC Bioinformatics
+Published-Year: 2001
+Published-DOI: 12:38doi:10.1186/1471-2105-12-38
+
+Depends: disulfinder
+Published-Title: DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.
+Published-Authors: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi
+Published-In: Nucleic Acids Res. 34:W177-81
+Published-Year: 2006
+Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986
+Published-PubMed: 19378139
+
+Suggests: circos
+
+Depends: populations
+
+Depends: raccoon
+
+Depends: librg-utils-perl
+
+Depends: snap
+Published-Authors: I. Korf
+Published-Title: Gene finding in novel Genomes
+Published-In: BMC Bioinformatics
+Published-DOI: doi:10.1186/1471-2105-5-59
+Published-URL: http://www.biomedcentral.com/1471-2105/5/59/abstract
+Published-Year: 2004
+
+Depends: vcftools
+
+Suggests: mobyle
+License: GPL-2+
+WNPP: 637230
+Homepage: https://projets.pasteur.fr/projects/show/mobyle
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mobyle/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mobyle/trunk/
+Pkg-Description: Web portal  that provides web forms for command-line software.
+ Mobyle is a framework and web portal specifically aimed at the integration of
+ bioinformatics software and databanks. It generates a web interface from an xml
+ description for command-line based tools.
+ It can submit jobs locally or using DRM systems.
+
+Depends: hilbertvisgui
+Homepage: http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/HilbertVisGUI.html
+License: GPL-3
+Pkg-Description: interactive tool to visualize long vectors of integer data by means of Hilbert curves
+ An interactive tool to visualize long vectors of integer data by means of Hilbert
+ curves.  It provides a GUI for the Debian packaged r-bioc-hilbertvis and is thus
+ interesting for giving users some comfort.  Until this software is not yet packaged
+ you can follow the hint at the homepage how to use it with R.
+
+Depends: pal2nal
+WNPP: 604701
+Responsible: Steffen Moeller <moeller at debian.org>
+Homepage: http://www.bork.embl.de/pal2nal/
+License: to be clarified
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pal2nal/trunk/
+Pkg-Description: converts proteins to genomic DNA alignment
+ PAL2NAL is a program that converts a multiple sequence alignment
+ of proteins and the corresponding DNA (or mRNA) sequences into
+ a codon-based DNA alignment. The program automatically assigns
+ the corresponding codon sequence even if the input DNA sequence
+ has mismatches with the input protein sequence, or contains UTRs,
+ polyA tails. It can also deal with frame shifts in the input
+ alignment, which is suitable for the analysis of pseudogenes.
+ The resulting codon-based DNA alignment can further be subjected
+ to the calculation of synonymous (Ks) and non-synonymous (Ka)
+ substitution rates.
+Published-Title: PAL2NAL: robust conversion of protein sequence alignment into the corresponding codon alignments.
+Published-Authors: Mikita Suyama, David Torrents, and Peer Bork
+Published-In: Nucleic Acids Res. 34:W609-W612
+Published-Year: 2006
+
+Depends: sra-sdk
+Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software
+License: Public domain (U. S. A. governmental work)
+WNPP: 610603
+Responsible: Charles Plessy <plessy at debian.org>
+Language: C
+Pkg-Description: utilities for the NCBI Sequence Read Archive
+ Tools for reading the SRA archive, generally by converting individual runs
+ into some commonly used format such as fastq. It also includes sources to
+ loader tools that are still under test. The intention is to give pre-release
+ access to the reader code.
+ .
+ The textual dumpers "sra-dump" and "vdb-dump" are provided in this
+ release as an aid in visual inspection. It is likely that their
+ actual output formatting will be changed in the near future to a
+ stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON
+ THE OUTPUT FORMAT SEEN IN THIS RELEASE.
+ .
+ The "help" information will be improved in near future releases, and
+ the tool options will become standardized across the set. We will
+ also be providing documentation on our web site.
+ .
+ Tool options may change in the next release. Version 1 tool options
+ will remain supported wherever possible in order to preserve
+ operation of any existing scripts.
+
+
+Depends: pcma
+Homepage: ftp://iole.swmed.edu/pub/PCMA/
+License: non-free for commercial
+Enhances: t-coffee
+Pkg-Description: fast and accurate multiple sequence alignment based on profile consistency
+ PCMA (profile consistency multiple sequence alignment) is a progressive
+ multiple sequence alignment program that combines two different
+ alignment strategies. Highly similar sequences are aligned in a fast way
+ as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is
+ applied to align the relatively divergent groups based on
+ profile–profile comparison and consistency. The scoring function for
+ local alignments of pre-aligned groups is based on a novel
+ profile–profile comparison method that is a generalization of the
+ PSI-BLAST approach to profile–sequence comparison. PCMA balances speed
+ and accuracy in a flexible way and is suitable for aligning large
+ numbers of sequences.
+Published-URL: http://bioinformatics.oxfordjournals.org/content/19/3/427.short
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+ .
+ Check with authors about licensing, they adopted code from clustalw which is now
+ free.  Thus a change might be possible
+
+Depends: fas
+Homepage: http://fsa.sourceforge.net/
+License: GPL v3
+Enhances: t-coffee
+Pkg-Description: Fast Statistical Alignment
+ FSA is a probabilistic multiple sequence alignment algorithm which uses
+ a "distance-based" approach to aligning homologous protein, RNA or DNA
+ sequences. Much as distance-based phylogenetic reconstruction methods
+ like Neighbor-Joining build a phylogeny using only pairwise divergence
+ estimates, FSA builds a multiple alignment using only pairwise
+ estimations of homology. This is made possible by the sequence annealing
+ technique for constructing a multiple alignment from pairwise
+ comparisons, developed by Ariel Schwartz in  "Posterior Decoding Methods
+ for Optimization and Control of Multiple Alignments."
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+
+Depends: sap
+Homepage: http://mathbio.nimr.mrc.ac.uk/wiki/Software#SAP
+License: GPL v3
+Enhances: t-coffee
+Pkg-Description: Pairwise protein structure alignment via double dynamic programming
+ In contrast to DNA, proteins exhibit an apparently unlimited variety of
+ structure. This is a necessary requirement of the vast array of
+ differing functions that they perform in the maintainance of life,
+ again, in contrast to the relatively static archival function of DNA.
+ Not only do we observe a bewildering variety of form but even within a
+ common structure, there is variation in the lengths and orientation
+ substructures. Such variation is both a reflection on the very long time
+ periods over which some structures have diverged and also a consequence
+ of the fact that proteins cannot be completely rigid bodies but must
+ have flexibility to accommodate the structural changes that are almost
+ always necessary for them to perform their functions. These aspects make
+ comparing structure and finding structural similarity over long
+ divergence times very difficult. Indeed, computationally, the problem of
+ recognizing similarity is one of three-dimensional pattern recognition,
+ which is a notoriously difficult problem for computers to perform. In
+ this chapter, guidance is provided on the use of a flexible structure
+ comparison method that overcomes many of the problems of comparing
+ protein structures that may exhibit only weak similarity.
+Published-URL: http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-368-2:19
+Remark: Precondition for T-Coffee
+ see http://wiki.debian.org/DebianMed/TCoffee
+
+Depends: clonalorigin
+Homepage: http://code.google.com/p/clonalorigin/
+License: GPLv3
+Pkg-Description: inference of homologous recombination in bacteria using whole genome sequences
+ Bacteria, unlike us, can reproduce on their own. They do however have
+ mechanisms that transfer DNA between organisms, a process more formally
+ known as recombination. The mechanisms by which recombination takes
+ place have been studied extensively in the laboratory but much remains
+ to be understood concerning how, when and where recombination takes
+ place within natural populations of bacteria and how it helps them to
+ adapt to new environments. ClonalOrigin performs a comparative analysis
+ of the sequences of a sample of bacterial genomes in order to
+ reconstruct the recombination events that have taken place in their
+ ancestry.
+Published-URL: http://www.genetics.org/cgi/content/abstract/genetics.110.120121v1
+
+Depends: zodiac
+Homepage: http://www.zeden.org/
+License: GPL
+WNPP: 613528
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/zodiac-zeden/trunk/
+Vcs-Svn: http://svn.debian.org/debian-med/trunk/packages/zodiac-zeden/trunk/
+Language: C, C++
+Responsible: Alex Mestiashvili <alexander.mestiashvili at biotec.tu-dresden.de>
+Pkg-Description: Zeden's Organise DIsplay And Compute
+ Zodiac is a molecular modelling suite for computation, analysis and
+ display of molecular data. It features state-of-the-art tools for
+ managing molecular databases, run molecular docking experiments, compute
+ raytraced images and much more.
+
+Depends: beads
+Homepage: http://pappso.inra.fr/bioinfo/beads
+License: CeCILL
+Pkg-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages
+Pkg-Description: 2-DE electrophoresis gel image spot detection
+ BEADS is a program for spot detection on 2-D gel images. It is based on
+ an analogy with beads flowing uphill on the surface of the gel image and
+ on the analysis of their paths
+
+Depends: x-tandem-pipeline
+Homepage: http://pappso.inra.fr/bioinfo/xtandempipeline/
+License: GPL
+Language: Java
+Pkg-Description: peptide/protein identification from MS/MS mass spectra
+ X!Tandem is an open-source software performing peptide/protein
+ identification from MS/MS mass spectra. X!Tandem is fast and accurate,
+ but the Global Proteome Machine (GPM) is relatively limited regarding
+ the processing of identification results. X!Tandem pipeline is an
+ alternative to the installation of the GPM on local servers.  X!Tandem
+ pipeline performs database searching and matching on a list of MS/MS
+ runs in one shot, using a list of easily user selected paramaters and
+ databases.  X!Tandem pipeline also performs filtering of data according
+ to statistical values at peptide and protein levels. The results are
+ stored into TSV (Tab Separated Values) files. Moreover, redundancy of
+ protein databases are fully filtered as follows :
+  * proteins identified without specific peptides compared to others are
+    eliminated;
+  * proteins identified with the same pool of peptides are assembled;
+  * proteins are grouped by function (identified with at least one common
+    peptide), and the specific peptides for each sub-group of proteins are
+    indicated.
+
+Suggests: maude
+WNPP: 611927
+
+Depends: forge
+Homepage: http://combiol.org/forge/
+License: Apache 2.0
+Pkg-Description: genome assembler for mixed read types
+ Forge Genome Assembler is a parallel, MPI based genome assembler for
+ mixed read types.
+ .
+ Forge is a classic "Overlap layout consensus" genome assembler written
+ by Darren Platt and Dirk Evers. Implemented in C++ and using the
+ parallel MPI library, it runs on one or more machines in a network and
+ can scale to very large numbers of reads provided there is enough
+ collective memory on the machines used. It generates a full consensus
+ alignment of all reads, can handle mixtures of sanger, 454 and illumina
+ reads. There is some support for solid color space and it includes built
+ in tools for vector trimming and contamination screening.
+ .
+ Forge and was originally developed at Exelixis and they have kindly
+ agreed to place the software which underwent much subsequent development
+ outside Exelixis, into the public domain. Forge works with most of the
+ common MPI implementations.
+Remark: Competitor to MIRA2 and wgs-assembler
+ This package was requested by William Spooner <whs at eaglegenomics.com> as
+ a competitor to MIRA2 and wgs-assembler.
+
+Depends: rdp-classifier
+Homepage: http://rdp.cme.msu.edu/
+License: GPL-2+
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rdp-classifier/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rdp-classifier/trunk/
+Pkg-Description: taxonomic assignment from next generation sequencing
+ The RDP Classifier is a nave Bayesian classifier that can rapidly and
+ accurately provides taxonomic assignments from domain to genus, with
+ confidence estimates for each assignment.
+
+Depends: fasttree
+Homepage: http://www.microbesonline.org/fasttree/
+License: GPL-2+
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/fasttree/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/fasttree/trunk/
+Pkg-Description: phylogenetic trees from alignments of nucleotide or protein sequences
+ FastTree infers approximately-maximum-likelihood phylogenetic trees from
+ alignments of nucleotide or protein sequences. It handles alignments
+ with up to a million of sequences in a reasonable amount of time and
+ memory. For large alignments, FastTree is 100-1,000 times faster than
+ PhyML 3.0 or RAxML 7.
+ .
+ FastTree is more accurate than PhyML 3 with default settings, and much
+ more accurate than the distance-matrix methods that are traditionally
+ used for large alignments. FastTree uses the Jukes-Cantor or generalized
+ time-reversible (GTR) models of nucleotide evolution and the JTT
+ (Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
+ for the varying rates of evolution across sites, FastTree uses a single
+ rate for each site (the "CAT" approximation). To quickly estimate the
+ reliability of each split in the tree, FastTree computes local support
+ values with the Shimodaira-Hasegawa test (these are the same as PhyML
+ 3's "SH-like local supports").
+
+Depends: microbiomeutil
+Homepage: http://microbiomeutil.sourceforge.net/
+License: free
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/microbiomeutil/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/microbiomeutil/trunk/
+Pkg-Description: Microbiome Analysis Utilities
+ The microbiomeutil package comes with the following utilities:
+  * ChimeraSlayer:  ChimeraSlayer for chimera detection.
+  * NAST-iEr:       NAST-based alignment tool.
+  * WigeoN:         A reimplementation of the Pintail 16S anomaly
+                    detection utility
+  * RESOURCES:      Reference 16S sequences and NAST-alignments that
+                    the tools above leverage.
+
+Depends: soapdenovo
+Homepage: http://soap.genomics.org.cn/soapdenovo.html
+License: GPL-3
+Pkg-Description: short-read assembly method for human-sized genomes
+ SOAPdenovo is a novel short-read assembly method that can build a de
+ novo draft assembly for the human-sized genomes. The program is
+ specially designed to assemble Illumina GA short reads. It creates new
+ opportunities for building reference sequences and carrying out accurate
+ analyses of unexplored genomes in a cost effective way.
+
+Depends: metarep
+License: MIT
+Homepage: http://www.jcvi.org/metarep/
+Pkg-Description: JCVI Metagenomics Reports
+ JCVI Metagenomics Reports (METAREP) is a new open source tool for
+ high-performance comparative metagenomics. It provides a suite of web
+ based tools to help scientists to view, query, browse and compare
+ metagenomics annotation data derived from ORFs called on metagenomics
+ reads.
+ .
+ METAREP supports browsing of functional and taxonomic assignments.
+ Users can either specify fields, or logical combinations of fields to
+ flexibly filter datasets on the fly. Users can compare multiple datasets
+ at various functional and taxonomic levels applying statistical tests as
+ well as hierarchical clustering, multidimensional scaling and heatmaps.
+
+Depends: smalt
+License: "shortly" under GPL
+Homepage: http://www.sanger.ac.uk/resources/software/smalt/
+Pkg-Description: align DNA sequencing reads with genomic reference sequences
+ SMALT reads from a range of sequencing platforms, for example Illumina-Solexa,
+ Roche-454 or ABI-Sanger, can be processed including paired-end reads.
+ .
+ The software employs a perfect hash index of short words (< 20
+ nucleotides long), sampled at equidistant steps along the genomic
+ reference sequences.
+ .
+ For each read, potentially matching segments in the reference are
+ identified from seed matches in the index and subsequently aligned with
+ the read using a banded Smith-Waterman algorithm.
+ .
+ The best gapped alignments of each read is reported including a score
+ for the reliability of the best mapping. The user can adjust the
+ trade-off between sensitivity and speed by tuning the length and spacing
+ of the hashed words.
+ .
+ A mode for the detection of split (chimeric) reads is provided.
+ Multi-threaded program execution is supported.
+Remark: This can be regarded as successor of ssaha2
+ This program is from the same author as ssaha2 and according to its author
+ faster and more precise than ssaha2 (except for sequences > 2000bp).
+
+
+X-Comment: Not sure whether this can be distributed at all - asking
+ might not harm because I've got a serious hint that this software
+ is quite interesting
+X-Depends: megan
+X-License: Registriation required
+X-Homepage: http://www-ab.informatik.uni-tuebingen.de/software/megan
+X-Pkg-Description: MEtaGenome ANalyzer
+ In metagenomics, the aim is to understand the composition and operation
+ of complex microbial consortia in environmental samples through
+ sequencing and analysis of their DNA. Similarly, metatranscriptomics and
+ metaproteomics target the RNA and proteins obtained from such samples.
+ Technological advances in next-generation sequencing methods are fueling
+ a rapid increase in the number and scope of environmental sequencing
+ projects. In consequence, there is a dramatic increase in the volume of
+ sequence data to be analyzed.
+
+Depends: ray-denovoassembler
+Homepage: http://sourceforge.net/projects/denovoassembler/
+License: GPLv3
+Pkg-Description: computes de novo genome assemblies of next-gen sequencing data
+ Ray is a paralleled computer-controlled software that computes de novo
+ genome assemblies of next-gen sequencing data using message passing
+ interface.
+Published-doi: 10.1089/cmb.2009.0238
+
+Depends: arachne
+Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
+License: free
+Pkg-Description: toolkit for Whole Genome Shotgun Assembly
+ Arachne is a toolkit developed for Whole Genome Shotgun Assembly.
+ Arachne consists of a comprehensive set of modules, including a central
+ pipeline (Assemblez) that can be run on almost any genome to produce a
+ draft assembly. Arachne's mandate explicitly includes accommodating
+ difficult genomes with complications such as extreme size, repeats, and
+ high polymorphism rates. In order to construct a reasonably
+ well-connected assembly from such tricky genomes, Arachne provides
+ further tools that can be used after the main module pipeline.
+ .
+ The Arachne code package has been under continuous development since
+ 2000. It began with the classic "overlap-layout-consensus" paradigm and
+ has since developed into a vast collection of tools, implemented in
+ numerous modules, to analyze, visualize and manipulate assemblies. New
+ and improved algorithms are becoming available on a regular basis.
+
+Depends: maker2
+Homepage: http://www.yandell-lab.org/software/maker.html
+License: GPL / Artistic
+Pkg-Description: annotate genomes and create genome databases
+ MAKER is a portable and easily configurable genome annotation pipeline.
+ It's purpose is to allow smaller eukaryotic and prokaryotic genome
+ projects to independently annotate their genomes and to create genome
+ databases. MAKER identifies repeats, aligns ESTs and proteins to a
+ genome, produces ab-initio gene predictions and automatically
+ synthesizes these data into gene annotations having evidence-based
+ quality values. MAKER is also easily trainable: outputs of preliminary
+ runs can be used to automatically retrain its gene prediction algorithm,
+ producing higher quality gene-models on seusequent runs. MAKER's inputs
+ are minimal and its ouputs can be directly loaded into a GMOD database.
+ They can also be viewed in the Apollo genome browser; this feature of
+ MAKER provides an easy means to annotate, view and edit individual
+ contigs and BACs without the overhead of a database. MAKER should prove
+ especially useful for emerging model organism projects with minimal
+ bioinformatics expertise and computer resources
+
+Depends: repeatmasker
+Homepage: http://www.repeatmasker.org/
+License: Open Software License v. 2.1
+Pkg-Description: screens DNA sequences for interspersed repeats
+ RepeatMasker is a program that screens DNA sequences for interspersed
+ repeats and low complexity DNA sequences. The output of the program is a detailed
+ annotation of the repeats that are present in the query sequence as well as a
+ modified version of the query sequence in which all the annotated repeats have
+ been masked (default: replaced by Ns). On average, almost 50% of a human genomic
+ DNA sequence currently will be masked by the program. Sequence comparisons in
+ RepeatMasker are performed by one of several popular search engines including,
+ cross_match, ABBlast/WUBlast, RMBlast and Decypher.
+
+Depends: trf
+Homepage: http://tandem.bu.edu/trf/trf.html
+License: binary only (non-free)
+Pkg-Description: Tandem Repeats Finder
+ A tandem repeat in DNA is two or more adjacent, approximate copies of a
+ pattern of nucleotides. Tandem Repeats Finder is a program to locate and
+ display tandem repeats in DNA sequences. In order to use the program, the
+ user submits a sequence in FASTA format. There is no need to specify the
+ pattern, the size of the pattern or any other parameter. The output consists
+ of two files: a repeat table file and an alignment file. The repeat table
+ contains information about each repeat, including its location, size,
+ number of copies and nucleotide content. Clicking on the location indices
+ for one of the table entries opens a second web browser that shows an
+ alignment of the copies against a consensus pattern. The program is very
+ fast, analyzing sequences on the order of .5Mb in just a few seconds.
+ Submitted sequences may be of arbitrary length. Repeats with pattern size
+ in the range from 1 to 2000 bases are detected. Sequence information sent
+ to the server is confidential and deleted after program execution.
+Published-Title: Tandem repeats finder: a program to analyze DNA sequences
+Published-Authors: G. Benson
+Published-In: Nucleic Acids Research
+Published-Year: 1999
+
+Depends: rmblast
+Homepage: http://tandem.bu.edu/trf/trf.html
+License: Same as blast2
+Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST
+ RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST
+ suite. The primary difference between this distribution and the NCBI
+ distribution is the addition of a new program "rmblastn" for use with
+ RepeatMasker and RepeatModeler.
+ RMBlast supports RepeatMasker searches by adding a few necessary features
+ to the stock NCBI blastn program. These include: Support for custom matrices
+ ( without KA-Statistics ). Support for cross_match-like complexity adjusted
+ scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
+ Support for cross_match-like masklevel filtering.
+
+Depends: augustus
+Homepage: http://augustus.gobics.de/
+License: not explicitely specified
+Pkg-Description: predict genes in eukaryotic genomic sequences
+ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+ It can be run on this web server or be downloaded and run locally. It is
+ open source so you can compile it for your computing platform. You can now
+ run AUGUSTUS on the German MediGRID. This enables you to submit larger
+ sequence files and allows to use protein homology information in the
+ prediction. The MediGRID requires an instant easy registration by email
+ for first-time users.
+
+Depends: mugsy
+Homepage: http://mugsy.sourceforge.net/
+License: Artistic License 2.0
+Pkg-Description: multiple whole genome aligner
+ Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise
+ alignment, a custom graph based segmentation procedure for identifying
+ collinear regions, and the segment-based progressive multiple alignment
+ strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form
+ of multi-FASTA files and does not require a reference genome.
+Published-Title: Mugsy: fast multiple alignment of closely related whole genomes
+Published-Authors: Angiuoli SV, Salzberg SL
+Published-In: Bioinformatics
+Published-Year: 2011
+
+Depends: apollo
+Homepage: http://gmod.org/wiki/Apollo
+License: Artistic License
+Pkg-Description: genome annotation viewer and editor
+ Apollo is a genome annotation viewer and editor. It was developed as a
+ collaboration between the Berkeley Drosophila Genome Project (part of
+ the FlyBase consortium) and The Sanger Institute in Cambridge, UK.
+ Apollo allows researchers to explore genomic annotations at many levels
+ of detail, and to perform expert annotation curation, all in a graphical
+ environment. It was used by the FlyBase biologists to construct the
+ Release 3 annotations on the finished Drosophila melanogaster genome,
+ and is also a primary vehicle for sharing these annotations with the
+ community. The Generic Model Organism Database (GMOD) project, which
+ aims to provide a complete ready-to-use toolkit for analyzing whole
+ genomes, has adopted Apollo as its annotation workbench. Apollo is a
+ Java application that can be downloaded and run on Windows, Mac OS X,
+ or any Unix-type system (including Linux).
+Published-Title: Apollo: a sequence annotation editor
+Published-Authors: Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Ricter J, Wiel C, Bayraktaroglu L, Birney E, Crosby MA, Kaminker JS, Matthews B, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME
+Published-In: Genome Biology
+Published-Year: 2002
+
+Depends: e-hive
+Homepage: http://www.ensembl.org/info/docs/eHive/index.html
+License: Not specified
+Pkg-Description: distributed processing system based on 'autonomous agents'
+ This is a distributed processing system based on 'autonomous agents' and
+ Hive behavioural structure of Honey Bees .  It implements all functionality
+ of both data-flow graphs and block-branch diagrams which should allow it
+ to codify any program, algorithm, or parallel processing job control system.
+ It is not bound to any processing 'farm' system and can be adapted to any GRID.
+
+Depends: chado
+Homepage: http://gmod.org/wiki/Chado
+License: Not specified
+Pkg-Description: relational database schema for data frequently encountered in modern biology
+ Chado is a relational database schema that underlies many GMOD installations.
+ It is capable of representing many of the general classes of data frequently
+ encountered in modern biology such as sequence, sequence comparisons,
+ phenotypes, genotypes, ontologies, publications, and phylogeny. It has been
+ designed to handle complex representations of biological knowledge and should
+ be considered one of the most sophisticated relational schemas currently
+ available in molecular biology.
+
+Depends: cmap
+Homepage: http://gmod.org/wiki/CMap
+License: Not specified
+Pkg-Description: view comparisons of genetic and physical maps
+ CMap is a web-based tool that allows users to view comparisons of genetic and
+ physical maps. The package also includes tools for curating map data.
+
+Depends: gbrowse-syn
+Homepage: http://gmod.org/wiki/GBrowse_syn
+License: Not specified
+Pkg-Description: Generic Synteny Browser
+ GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny
+ browser designed to display multiple genomes, with a central reference
+ species compared to two or more additional species.  It can be used to
+ view multiple sequence alignment data, synteny or co-linearity data
+ from other sources against genome annotations provided by GBrowse.
+ GBrowse_syn is included with the standard GBrowse package (version 1.69 and
+ later). Working examples can be seen at TAIR and WormBase.
+
+Depends: jbrowse
+Homepage: http://gmod.org/wiki/JBrowse
+License: Not specified
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/jbrowse/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/jbrowse/
+Pkg-Description: genome browser with an AJAX-based interface
+ JBrowse is a genome browser with an AJAX-based interface. JBrowse renders most
+ tracks using client side JavaScript and JSON as its data transfer format.
+ JBrowse is the official successor to GBrowse.
+
+Depends: tripal
+Homepage: http://www.genome.clemson.edu/software/tripal
+License: GPL ( as Drupal a derivative )
+Pkg-Description: collection of Drupal modules for genomic research
+ Tripal is a collection of open-source freely available Drupal modules under
+ development at CUGI and a member of the GMOD family of tools. Tripal serve
+ as a web interface for the GMOD Chado database. Tripal intially started as
+ a web front-end for the Marine Genomics Project (MG.org). Work on the
+ interface is currently ongoing for the MG.org project as well as the
+ Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being
+ implemented for the new Cacao Genome Database, and Citrus Genome Database
+ and will be used for the Genome Database for Rosaceae. These latter three
+ databases are projects of the Main Bioinformatics Laboratory at Washington
+ State University
+
+Depends: genemark
+Homepage: http://exon.biology.gatech.edu/
+License: Academic License Agreement
+Pkg-Description: family of gene prediction programs
+ A family of gene prediction programs developed at Georgia Institute of
+ Technology, Atlanta, Georgia, USA.
+
+Depends: strap
+Homepage: http://3d-alignment.eu/
+License: GNU + some external components with different licenses
+Language: Java
+Pkg-Description: Interactive Structure based Sequences Alignment Program
+ STRAP is a comfortable and comprehensive tool to edit multiple protein
+ sequence alignments. A wide range of functions related to protein
+ sequences and protein structures are accessible with an intuitive
+ graphical interface.
+ .
+ STRAP is tightly integrated into your desktop environment supporting
+ cut&paste, word completion and spell check. Drag_and_drop is
+ available for proteins, nucleotide structures and hetero structures.
+ Context menu for proteins, annotations and files are triggered by
+ right mouse click. The program appears to be complicated in the
+ beginning. With the help of the integrated tutorials you will learn how
+ to apply the currently available methods to compare proteins sequences
+ and structures.
+ .
+ Key features are:
+  * Visualization and manipulation of sequence alignments (up to 1000
+    sequences)
+  * Automatic computation of multiple sequence alignments by Clustalw
+  * Loading protein files from public databases
+  * BLAST searches
+  * Structure prediction
+  * 3D-visualization using either PyMol, Rasmol, VMD, JMol
+  * 3D-superposition of C-alpha atoms
+  * Dot-plots
+  * High quality PDF output by LaTeX/TeXshade
+  * Project safety by included backup system
+  * Translation of nucleotide sequences to amino acid sequences
+  * Residue selections
+
+Depends: cinema
+License: LGPL
+Language: Java
+Homepage: http://www.bioinf.man.ac.uk/dbbrowser/ALIGN/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cinema/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cinema/trunk/
+Pkg-Description: multi-sequence alignment editor and viewer.
+ It has been designed to be as extensible as possible. Notes of this
+ extensibility can be found in "EXTENDING_CINEMA", and the
+ "cinema-module" sub-directory.
+ .
+ Cinema currently has limited support for various sequence formats,
+ although its easy to add new ones. A large number of alignments in the
+ appropriate format can be found as part of the align compendium at
+
+Suggests: python-rdkit
+
+Depends: python-orange
+License: GPLv3
+Homepage: http://orange.biolab.si/
+Pkg-URL: http://orange.biolab.si/debian/
+Responsible: Mitar <mmitar at gmail.com>
+Pkg-Description: Data mining framework
+ Orange is a component-based data mining software. It includes a range
+ of data visualization, exploration, preprocessing and modeling
+ techniques. It can be used through a nice and intuitive user interface
+ or, for more advanced users, as a module for Python programming language.
+
+Depends: python-reaper
+Homepage: http://qtlreaper.sf.net
+License: GPL-2+
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qtlreaper/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/qtlreaper/trunk/
+Pkg-Description: QTL analysis for expression data
+ QTL Reaper is software, written in C and compiled as a Python module, for
+ rapidly scanning microarray expression data for QTLs. It is essentially
+ the batch-oriented version of WebQTL. It requires, as input, expression
+ data from members of a set of recombinant inbred lines and genotype
+ information for the same lines. It searches for an association between
+ each expression trait and all genotypes and evaluates that association
+ by a permutation test. For the permutation test, it performs only as
+ many permutations as are necessary to define the empirical P-value to a
+ reasonable precision. It also performs bootstrap resampling to estimate
+ the confidence region for the location of a putative QTL.
+ .
+ The reaper module is used underneath the http://genenetwork.org site.
+
+Depends: anfo
+Homepage: http://bioinf.eva.mpg.de/anfo/
+License: GPLv3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/anfo/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/anfo/trunk/
+Pkg-Description: Short Read Aligner/Mapper from MPG
+ Anfo is a mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes
+ more after BLAST/BLAT. It's most useful for the alignment of sequencing reads
+ where the DNA sequence is somehow modified (think ancient DNA or bisulphite
+ treatment) and/or there is more divergence between sample and reference than
+ what fast mappers will handle gracefully (say the reference genome is missing
+ and a related species is used instead).
+
+Depends: plato
+Homepage: https://chgr.mc.vanderbilt.edu/plato
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plato/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plato/trunk
+License: GPL-2+
+Pkg-Description: Analysis, translation, and organization of large-scale genetic data
+ PLATO is an acronym for "PLatform for the Analysis, Translation,
+ and Organization of large-scale data".  Recent technological advances
+ enable the study of hundreds of thousands of human single-nucleotide
+ polymorphisms at the population level. Because strategies for analyzing
+ these data have not kept pace with the laboratory methods that generate
+ the data, it is unlikely that these advances will immediately lead to
+ an improved understanding of the genetic contribution to common human
+ disease and drug response. Currently, no single analytical method
+ allows us to extract all available information from a whole-genome
+ association study. In fact, no single method can be optimal for all
+ datasets, especially when the genetic architecture for diseases can
+ vary substantially, as is certainly the case. Therefore, an integrative
+ platform is needed to accommodate multiple analytical methods for
+ analysis as we learn more about genetic architecture. As a result,
+ we are developing a system for the analysis of genome-wide association
+ data that will incorporate several analytical approaches as filters to
+ allow a scientist to choose whatever analytical methods they wish to
+ apply. PLATO (PLatform for the Analysis, Translation, and Organization
+ of large-scale data) will incorporate a number of filters to select
+ the important SNPs in a genome-wide association study.
+ .
+ Whole-genome Association Study Pipeline (WASP) has recently been
+ absorbed into PLATO. WASP was designed to aid in retrieving, evaluating,
+ formatting, and analyzing genotypic and clinical data from the latest
+ large-scale genotyping studies. WASP implements a battery of quality
+ control procedures to assess the data. Among the currently available
+ procedures are the examination of marker and sample genotyping
+ efficiency, allele frequency calculations, checks of Mendelian error
+ (if applicable) and gender discrepancies (based on available chromosome X
+ and Y genotypes), and tests of Hardy-Weinberg Equilibrium. Additionally,
+ WASP can retrieve and format data for other software programs such as the
+ Graphical Representation of Relationships (GRR) program, or STRUCTURE,
+ and depending on the nature of the samples and the depth of examination
+ the user desires to pursue. Beyond the quality control aspect of this
+ application, WASP can perform standard tests of association using the
+ Transmission Disequilibrium Test TDT for family-based datasets and the
+ chi-square test of association for case-control datasets.
+
+Suggests: eigensoft
+License: nonfree
+Homepage: http://www.hsph.harvard.edu/faculty/alkes-price/software/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/eigensoft/trunk
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/eigensoft/trunk/
+Pkg-Description: reduction of population bias for genetic analyses
+ The EIGENSOFT package combines functionality from the group's population
+ genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
+ method (Price et al. 2006). The EIGENSTRAT method uses principal components
+ analysis to explicitly model ancestry differences between cases and
+ controls along continuous axes of variation; the resulting correction is
+ specific to a candidate marker's variation in frequency across ancestral
+ populations, minimizing spurious associations while maximizing power to
+ detect true associations. The EIGENSOFT package has a built-in plotting
+ script and supports multiple file formats and quantitative phenotypes.
+
+Suggests: cain
+License: BSD like
+Homepage: http://cain.sourceforge.net
+Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/cain/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cain/trunk/
+Pkg-Description: simulations of chemical reactions
+ Cain performs stochastic and deterministic simulations of chemical reactions.
+ It can spawn multiple simulation processes to utilize multi-core computers.
+ It stores models, methods, and simulation output (populations and reaction
+ counts) in an XML format. In addition, SBML models can be imported and
+ exported. The models and methods can be read from input files or edited
+ within the program.
+ .
+ The GUI (Graphical User Interface) is written in Python and uses the wxPython
+ toolkit. Most of the solvers are implemented as command line executables,
+ written in C++, which are driven by Cain. This makes it easy to launch batch
+ jobs. It also simplifies the process of adding new solvers. Cain offers a
+ variety of solvers:
+  * Gillespie's direct method.
+  * Gillespie's first reaction method.
+  * Gibson and Bruck's next reaction method.
+  * Tau-leaping.
+  * Hybrid direct/tau-leaping.
+  * ODE integration.
+
+Depends: sequenceconverter.app
+Homepage: http://bioinformatics.org/biococoa/
+License: GPL
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sequenceconverter/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/sequenceconverter/trunk/
+Pkg-Description: biological sequence file format conversion applet for GNUstep
+ Demo application to demonstrate the possibilities of the BioCocoa framework.
+ .
+ SequenceConverter is a GNUstep applet to convert between sequence file formats.
+ The BioCocoa framework provides developers with the opportunity to add
+ support for reading and writing BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE,
+ Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and
+ TNT files by writing only three lines of code. The framework is written in
+ Cocoa (Objective-C).
+Remark: Formerly part of Debian as biococoa.app but removed
+ The package was part of Debian under the name biococoa.app which is confusing
+ because biococoa is actually a library for working with sequences under GNUstep.
+ There was an attempt to reupload under the name sequenceconverter.app but
+ ftpmaster did not accepted the package.  The reasons can be read here:
+  http://lists.alioth.debian.org/pipermail/debian-med-packaging/2009-May/003430.html
+ .
+ Version 1.6 is the last upstream version that works with GNUstep.  If
+ newer versions are needed to work under Linux try to convince upstream to
+ support GNUstep.
+
+Depends: neobio
+Homepage: http://neobio.sourceforge.net/
+WNPP: 647543
+Responsible: "Dr. med. Christoph Gille" <christoph.gille at charite.de>
+Language: Java
+Pkg-Description: computes alignments of amino acid and nucleotide sequences
+ Library and graphical user interface for (pairwise) sequence
+ alignments. Implementation of the dynamic programming methods of
+ Needleman & Wunsch (global alignment) and Smith & Waterman (local
+ alignment).
+
+Depends: ugene
+Homepage: http://ugene.unipro.ru
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ugene/trunk
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ugene/trunk/
+
+Depends: vmd
+License: non-free
+Homepage: http://www.ks.uiuc.edu/Research/vmd/
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/wnpp/vmd/
+Vcs-Svn: svn://svn.debian.org/svn/debichem/wnpp/vmd/
+Responsible: Michael Banck <mbanck at debian.org>, Steffen Moeller <moeller at debian.org>
+Pkg-Description: presentation of traces of molecular dynamics runs
+ VMD stands for Visual Molecular Dynamics. While text books
+ and even structure databases because of technical problems only
+ present static pictures of proteins or DNA, for the understanding
+ of the properties of those molecules their vibration or their
+ movement in general is important.
+ .
+ The movements itself are calculated by molecular dynamics programs,
+ such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The
+ latter two are already in the distribution. VMD has a series of
+ nice features, from displaying through animation to analysing.
+ It can be scripted, clustered, and runs on all common OS.
+
+Depends: tophat
+License: Artistic
+Homepage: http://tophat.cbcb.umd.edu/
+Vcs-Git: git://git.debian.org/debian-med/tophat.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/tophat.git;a=summary
+Pkg-Description: TopHat is a fast splice junction mapper for RNA-Seq reads
+ It aligns RNA-Seq reads to mammalian-sized genomes using the ultra
+ high-throughput short read aligner Bowtie, and then analyzes the
+ mapping results to identify splice junctions between exons.
+ TopHat is a collaborative effort between the University of Maryland
+ Center for Bioinformatics and Computational Biology and the
+ University of California, Berkeley Departments of Mathematics and
+ Molecular and Cell Biology.
+
+Depends: reprof
+Responsible: Peter Hoenigschmid <hoenigschmid at rostlab.org>
+License: GPL-3
+WNPP: 655336
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/reprof/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/reprof/trunk/
+Homepage: http://rostlab.org/
+Pkg-Description: protein secondary structure and accessibility predictor
+ 'reprof' is an improved implementation of 'prof', a popular protein secondary
+ structure and accessibility predictor.  Prediction is either
+ done from protein sequence alone or from an alignment - the latter should be
+ used for optimal performance.
+ .
+ This package provides the 'reprof' command.  It is only a command line
+ interface to the functionality provided by the modules in
+ librg-reprof-bundle-perl.
+
+Depends: grinder
+Responsible: Florent Angly <florent.angly at gmail.com>
+Homepage: http://sourceforge.net/projects/biogrinder/
+Vcs-Git: git://git.debian.org/debian-med/grinder.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/grinder.git
+License: GPL-3+
+Pkg-Description: Versatile omics shotgun and amplicon sequencing read simulator
+ Grinder is a versatile program to create random shotgun and amplicon sequence
+ libraries based on DNA, RNA or proteic reference sequences provided in a
+ FASTA file.
+ .
+ Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,
+ proteomic, metaproteomic shotgun and amplicon datasets from current
+ sequencing technologies such as Sanger, 454, Illumina. These simulated
+ datasets can be used to test the accuracy of bioinformatic tools under
+ specific hypothesis, e.g. with or without sequencing errors, or with low or
+ high community diversity. Grinder may also be used to help decide between
+ alternative sequencing methods for a sequence-based project, e.g. should the
+ library be paired-end or not, how many reads should be sequenced.
+
+Depends: hhsuite
+Homepage: http://toolkit.genzentrum.lmu.de/sections/search
+License: GPL-3.0+
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/hhsuite/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/hhsuite/trunk/
+WNPP: 656626
+Responsible: Laszlo Kajan <lkajan at rostlab.org>
+Pkg-Description: sensitive protein sequence searching based on HMM-HMM alignment
+ HH-suite is an open-source software package for sensitive protein sequence
+ searching based on the pairwise alignment of hidden Markov models (HMMs).
+ It contains HHsearch and HHblits among other programs and utilities.
+ .
+ HHsearch takes as input a multiple sequence alignment (MSA) or profile HMM
+ and searches a database of HMMs (e.g. PDB, Pfam, or InterPro) for homologous
+ proteins. HHsearch is often used for protein structure prediction to detect
+ homologous templates and to build highly accurate query-template pairwise
+ alignments for homology modeling.
+ .
+ HHblits can build high-quality MSAs starting from single sequences or from
+ MSAs. It transforms these into a query HMM and, using an iterative search
+ strategy, adds significantly similar sequences from the previous search to
+ the updated query HMM for the next search iteration. Compared to PSI-BLAST,
+ HHblits is faster, up to twice as sensitive and produces more accurate
+ alignments.
+
+
+
+Comment: Several related R packages are listed at CRAN:
+         http://cran.r-project.org/web/views/Genetics.html
+Comment: There is a Gentoo page featuring some projects we do not have mentioned here:
+         http://gentoo-overlays.zugaina.org/dberkholz/sci-biology.html.en
+Comment: Phylogenie centric Ubuntu derivative with some additional derivatives
+	 http://www.eve.ucdavis.edu/rcthomson/phylis/
+Comment: SEQanswers: The next generation sequencing community
+	 http://seqanswers.com/forums/showthread.php?t=43
+Comment: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)