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@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: treeviewx
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: Computer Applications in the Bioscience 12:357-358
Published-Year: 1996

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, boxshade, gff2aplot, muscle, sim4, sibsim4, wise

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

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, clustalx
Why:         Sequence alignments and related programs (Non-free, thus only suggested).

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.

X-End-Category: Sequence alignments and related programs.

Depends:     last-align, maq, ssake, velvet
Why:         Tools related to 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, 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

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.

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:     sequenceconverter.app

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

PMID: 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: 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

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

Depends: bagphenotype
Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
License: GPL-3
Vcs-Svn: svn://svn.debian.org/svn/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/svn/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: r-other-genabel
Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
License: GPL 2+
WNPP: 492044
Vcs-Svn: svn://svn.debian.org/svn/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@debian.org>
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
Vcs-Svn: svn://svn.debian.org/svn/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: Steffen Moeller <moeller@debian.org>
License: non-free but redistributable
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@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
Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
License: GPL
X-Category: Phylogenetic analysis
X-Importance: Inference of large trees
Pkg-Description: Randomized Axelerated Maximum Likelihood
 RAxML is a program for sequential and parallel Maximum Likelihood-based
 inference of large phylogenetic trees. It has originally been derived
 from fastDNAml.
 .
 There are freely accessible web-servers available for RAxML at
 http://phylobench.vital-it.ch/raxml-bb/ and
 http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .

Depends: axparafit
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
Responsible: David Paleino <d.paleino@gmail.com>
License: GPL
Vcs-Svn: svn://svn.debian.org/svn/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@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@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@debian.org>
License: GPL and others
WNPP: 461504
X-Category: Motif detection
X-Importance: powerful
Vcs-Svn: svn://svn.debian.org/svn/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@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@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@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@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@debian.org>
License: GPL
WNPP: 500106
Vcs-Svn: svn://svn.debian.org/svn/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@debian.org>
License: GPL
Vcs-Svn: svn://svn.debian.org/svn/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@debian.org>
Vcs-Svn: svn://svn.debian.org/svn/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: jmol
Homepage: http://jmol.sourceforge.net/
Responsible: Michael Banck <mbanck@debian.org>
X-Old-Responsible: Vincent Fourmond <fourmond@debian.org>
License: LGPL
WNPP: 512930
Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/jmol/
Pkg-Description: viewer for chemical structures in 3D
 Jmol is a Java molecular viewer for three-dimensional chemical structures.
 Features include reading a variety of file types and output from quantum
 chemistry programs, and animation of multi-frame files and computed normal
 modes from quantum programs.  It includes with features for chemicals,
 crystals, materials and biomolecules.
  * The JmolApplet is a web browser applet that can be integrated into
    web pages.
  * The Jmol application is a standalone Java application that runs on
    the desktop.
  * The JmolViewer is a development tool kit that can be integrated into
    other Java applications.
X-Comment:
 For more detailed information about packaging status please see
 http://lists.debian.org/debian-med/2008/03/msg00097.html before
 you might download the source packages http://debian.wgdd.de/temp/jmol/

Depends: jtreeview
Homepage: http://jtreeview.sourceforge.net/
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL
WNPP: 243771
X-Category: Visualisation
Vcs-Svn: svn://svn.debian.org/svn/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: smile
Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Responsible: Steffen Moeller <moeller@debian.org>
WNPP: 221492
License: GPL
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/smile/trunk/
Pkg-Description: infer motifs in a set of sequences
 SMILE is a tool that infers motifs in a set of sequences, according to some
 criteria. It was first made to infer exceptional sites as binding sites in
 DNA sequences. Since the 1.4 version, 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.

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@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@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/
 does not seem to be available.

Depends: ngila
Homepage: http://scit.us/projects/ngila/
License: GPLv3
Responsible: Charles Plessy <plessy@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
Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
License: free to change and redistribute
Responsible: Steffen Moeller <moeller@debian.org>
WNPP: 447505
Pkg-Description: structural protein alignment
 TM-align is a structural alignment program for comparing two proteins
 whose sequences can be different. TM-align will first find the best
 equivalent residues of two proteins based on the structure similarity
 and then output a TM-score.
 .
 TM-align performs a structural alignment of protein sequences. It is
 said to be 10 times faster than DALI and no worse in accuracy.

Depends: dazzle
Homepage: http://www.biojava.org/dazzle
Responsible: Steffen Moeller <moeller@debian.org>
License: LGPL
Vcs-Svn: svn://svn.debian.org/svn/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@debian.org>
WNPP: 241195
License: GPL
Vcs-Svn: svn://svn.debian.org/svn/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@debian.org>
WNPP: 311421
License: DFSG free
Vcs-Svn: svn://svn.debian.org/svn/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@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@debian.org>
License: GPL
Pkg-URL: http://people.debian.org/~tille/packages/mauvealigner/
Vcs-Svn: svn://svn.debian.org/svn/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: gbrowse
Homepage: http://www.gmod.org/wiki/index.php/GBrowse
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 429610
License: Perl Artistic License, plus additional clauses
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gbrowse/trunk/
X-Category: Genome Browser
X-Importance: Academic ones are really expensive for commercial use
Pkg-Description: The Generic Genome Browser from GMOD
 The Generic Genome Browser is a combination of database and interactive Web
 page for manipulating and displaying annotations on genomes. Some of its
 features:
  * Simultaneous bird's eye and detailed views of the genome.
  * Scroll, zoom, center.
  * Attach arbitrary URLs to any annotation.
  * Order and appearance of tracks are customizable by administrator and end-user.
  * Search by annotation ID, name, or comment.
  * Supports third party annotation using GFF formats.
  * Settings persist across sessions.
  * DNA and GFF dumps.
  * Connectivity to different databases, including BioSQL and Chado.
  * Multi-language support.
  * Third-party feature loading.
  * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
    find oligonucleotides, design primers, create restriction maps, edit features)

Depends: mira
Homepage: http://chevreux.org/projects_mira.html
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 435915
License: GPL
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
Pkg-Description: Whole Genome Shotgun and EST Sequence Assembler
 The mira genome fragment assembler is a specialised assembler for
 sequencing projects classified as 'hard' due to high number of similar
 repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
 specialised on reconstructing pristine mRNA transcripts while
 detecting and classifying single nucleotide polymorphisms (SNP)
 occuring in different variations thereof.
 .
 The assembler is routinely used for such various tasks as mutation
 detection in different cell types, similarity analysis of transcripts
 between organisms, and pristine assembly of sequences from various
 sources for oligo design in clinical microarray experiments.
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: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 426489
License: GPL
X-Category: Graphical representation of sequence conservation
Language: Tcl/Tk
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/phylographer/trunk/
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).

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: seq-gen
Homepage: http://tree.bio.ed.ac.uk/software/seqgen/
License: Free
Pkg-Description: simulate the evolution of nucleotide or amino acid sequences
 Seq-Gen is a program that will simulate the evolution of nucleotide or
 amino acid sequences along a phylogeny, using common models of the
 substitution process. A range of models of molecular evolution are
 implemented including the general reversible model. State frequencies
 and other parameters of the model may be given and site-specific rate
 heterogeneity may also be incorporated in a number of ways. Any number
 of trees may be read in and the program will produce any number of data
 sets for each tree. Thus large sets of replicate simulations can be easily
 created. It has been designed to be a general purpose simulator that
 incorporates most of the commonly used (and computationally tractable)
 models of molecular sequence evolution.

Depends: wgs-assembler
Homepage: http://wgs-assembler.sourceforge.net/
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 395843
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: populations
Homepage: http://bioinformatics.org/~tryphon/populations/
License: GPL
Pkg-Description: individuals or populations distances based on allelic frequencies
 Population genetic software (individuals or populations distances, phylogenetic trees)
  * haploids, diploids or polyploids genotypes (see input formats)
  * structured populations (see input files structured populations
  * No limit of populations, loci, alleles per loci (see input formats)
  * Distances between individuals (15 different methods)
  * Distances between populations (15 methods)
  * Bootstraps on loci OR individuals
  * Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA
    (PHYLIP tree format)
  * Allelic diversity
  * Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
    Populations...)

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/?rev=0&sc=0
 .
 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.

Ignore: smile
Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
License: GPL
WNPP: 221492
Responsible: Steffen Moeller <moeller@debian.org>
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/smile/trunk/
Pkg-Description: Find statistically significant patterns in sequences
 Smile determines sequence motifs on the basis of a set of DNA, RNA or
 protein sequences. The work was originally described in the Journal of
 Computational Biology (2000) 7:345-362 and has since been developed
 further.
  * No hard limit on the number of combinations of motifs to describe
    subsets of sequences.
  * The sequence alphabet may be specified.
  * The use of wildcards is supported.
  * Better determination of significance of motifs by simulation.
  * Introduction of a set of sequences with negative controls
    that should not match automatically determined motifs.
 .
 Note: We do not know anybody who actually uses SMILE and thus the
 packaging effort is stalled.  Feel free to tell us, if you are
 interested in turning this into an official package.

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@debian.org>
Vcs-Svn: svn://svn.debian.org/svn/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/svn/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@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: transtermhp
Homepage: http://transterm.cbcb.umd.edu/index.php
License: Free
Pkg-Description: finds rho-independent transcription terminators in bacterial genomes
 finds rho-independent transcription terminators in bacterial
 genomes. Each terminator found by the program is assigned a
 confidence value that estimates its probability of being a true
 terminator. TransTermHP is described in: C. Kingsford, K. Ayanbule
 and S.L. Salzberg. Rapid, accurate, computational discovery of
 Rho-independent transcription terminators illuminates their
 relationship to DNA uptake. Genome Biology 8:R22 (2007).
Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)

Depends: patman
Homepage: http://bioinf.eva.mpg.de/patman/
License: GPL-2+
WNPP: 482555
Responsible: Charles Plessy <plessy@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@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@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@gmail.com>
Vcs-Svn: svn://svn.debian.org/svn/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@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@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@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@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@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@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@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@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: to be clarified
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
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.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

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@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: dotter
Homepage: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
License: to be clarified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: detailed comparison of two sequences
 Dotter is a graphical dotplot program for detailed comparison of two
 sequences.  Here, every residue in one sequence is compared to every
 residue in the other sequence. The first sequence runs along the
 x-axis and the second sequence along the y-axis. In regions where the
 two sequences are similar to each other, a row of high scores will
 run diagonally across the dot matrix. If you're comparing a sequence
 against itself to find internal repeats, you'll notice that the main
 diagonal scores maximally, since it's the 100% perfect self-match.
 .
 To make the score matrix more intelligible, the pairwise scores are
 averaged over a sliding window which runs diagonally. The averaged
 score matrix forms a three-dimensional landscape, with the two
 sequences in two dimensions and the height of the peaks in the
 third. This landscape is projected onto two dimensions by aid of
 greyscales - the darker grey of a peak, the higher it is.
 .
 Dotter provides a tool to explore the visual appearance of this
 landscape, as well as a tool to examine the sequence alignment it
 represents.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 .
 The package's homepage is currently unavailable but the source might be
 obtainable from freebsd.org.

Depends: dotur
Homepage: http://schloss.micro.umass.edu/software/dotur.html
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Defining Operational Taxonomic Units and estimating species Richness
 Dotur (Distance Based OTU and Richness determination) is a computer
 program that takes a distance matrix describing the genetic distance
 between DNA sequence data and assigns sequences to operational
 taxonomic units (OTUs) using either the furthest, average, or nearest
 neighbor algorithms for all possible distances that can be described
 using the distance matrix.  Using the OTU composition data, dotur
 constructs collector's and rarefaction curves for sampling intensity,
 richness estimators, and diversity indices.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: estferret
Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
License: to be clarified
Responsible: BioLinux - Bela Tiwari <btiwari@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@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@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@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@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@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@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@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@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@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@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: mrbayes
Homepage: http://mrbayes.csit.fsu.edu/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Bayesian estimation of phylogeny
 MrBayes is a program for the Bayesian estimation of
 phylogeny. Bayesian inference of phylogeny is based upon a quantity
 called the posterior probability distribution of trees, which is the
 probability of a tree conditioned on the observations. The
 conditioning is accomplished using Bayes's theorem. The posterior
 probability distribution of trees is impossible to calculate
 analytically; instead, MrBayes uses a simulation technique called
 Markov chain Monte Carlo (or MCMC) to approximate the posterior
 probabilities of trees.
 .
 The program takes as input a character matrix in a NEXUS file
 format. The output is several files with the parameters that were
 sampled by the MCMC algorithm. MrBayes can summarize the information
 in these files for the user. The program features include:
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@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@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@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@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: paml
Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
License: academics only (non-free)
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
WNPP: 595958
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Phylogenetic Analysis by Maximum Likelihood
 PAML is a package of programs for phylogenetic analyses of DNA or
 protein sequences using maximum likelihood. It is maintained and
 distributed for academic use free of charge by Ziheng Yang. ANSI C
 source codes are distributed for UNIX/Linux/Mac OSX, and executables
 are provided for MS Windows. PAML is not good for tree making. It may
 be used to estimate parameters and test hypotheses to study the
 evolutionary process, when you have reconstructed trees using other
 programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
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@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@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@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@ceh.ac.uk>
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

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@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@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@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@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@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@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@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@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@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@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/svn/debian-med/trunk/packages/kempbasu/trunk/
Responsible: Charles Plessy <plessy@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: fastx-toolkit
Homepage: http://hannonlab.cshl.edu/fastx_toolkit
License: AGPL / MIT
Responsible: Assaf Gordon <gordon@cshl.edu>
Pkg-Description: collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
 Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple
 short-reads sequences (possibly with quality information).  The main processing of such
 FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other
 databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP,
 LastZ, MAQ and many many others.
 .
 However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the
 sequences to the genome - manipulating the sequences to produce better mapping results.
 .
 The FASTX-Toolkit tools perform some of these preprocessing tasks.
Remark: See also
 http://hannonlab.cshl.edu/column_normalizer/
 .
 http://hannonlab.cshl.edu/crosstab/

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.

Suggests: pdb2pqr
Homepage: http://pdb2pqr.sourceforge.net/
License: GPL
WNPP: 416269
Language: Python, C
Responsible: Manuel Prinz <debian@pinguinkiste.de>
Pkg-Description: Converts Protein Data Bank (PDB) files to PQR
 "PDB2PQR is a Python software package that automates many of the
 common tasks of preparing structures for continuum electrostatics
 calculations. This includes adding a limited number of missing
 heavy atoms to biomolecular structures, optimizing the protein
 for favorable hydrogen bonding, determining side-chain pKas, and
 assigning charge and radius parameters from a variety of force
 fields, ultimately yielding a final PQR file."
 .
 PDB2PQR is a tool often used in conjunction with APBS, which is in
 Debian already. I have had good contact with both upstream authors
 in the past.

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: bowtie
Homepage: http://bowtie-bio.sourceforge.net/
License: Artistic
X-Category: Sequencing
Pkg-Description: An ultrafast memory-efficient short read aligner
 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
 DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
 reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep
 its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB
 for paired-end).

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: ncbi-tools++
Homepage: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
License: Public domain except for some third-party LGPLed code
Language: C++
WNPP: 150636
Pkg-Description: NCBI C++ libraries for biology applications
 The NCBI C++ Toolkit was developed for the production and distribution
 of new molecular-biology-related services by NCBI.  It allows you to
 read and write NCBI ASN.1 files, builds Cn3D, etc.

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: qiime
WNPP: 587275
Homepage: http://qiime.sf.net
License: GPL
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
Pkg-Description: Quantitative Insights Into Microbial Ecology
 QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
 microbial community analysis that integrates many third party tools which
 have become standard in the field. A standard QIIME analysis begins with
 sequence data from one or more sequencing platforms, including Sanger,
 Roche/454, and Illumina GAIIx. With all the underlying tools installed,
 of which not all are yet available in Debian (or any other Linux
 distribution), QIIME can perform library de-multiplexing and quality
 filtering; denoising with PyroNoise; OTU and representative set picking
 with uclust, cdhit, mothur, BLAST, or other tools; taxonomy assignment
 with BLAST or the RDP classifier; sequence alignment with PyNAST, muscle,
 infernal, or other tools; phylogeny reconstruction with FastTree, raxml,
 clearcut, or other tools; alpha diversity and rarefaction, including
 visualization of results, using over 20 metrics including Phylogenetic
 Diversity, chao1, and observed species; beta diversity and rarefaction,
 including visualization of results, using over 25 metrics including
 weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis;
 summarization and visualization of taxonomic composition of samples
 using pie charts and histograms; and many other features.
 .
 QIIME includes parallelization capabilities for many of the
 computationally intensive steps. By default, these are configured to
 utilize a mutli-core environment, and are easily configured to run in
 a cluster environment. QIIME is built in Python using the open-source
 PyCogent toolkit. It makes extensive use of unit tests, and is highly
 modular to facilitate custom analyses.

Depends: denoiser
WNPP: 587274
Homepage:  http://www.microbio.me/denoiser/
License: GPL
Language: Haskell
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/denoiser/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/denoiser/trunk/
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
Pkg-Description: Rapid denoising of pyrosequencing amplicon data
 To denoise pyrosequencing amplicon data, the package exploits the
 rank-abundance distribution.  PyroNoise uses an expectation maximization
 (EM) algorithm to figure out the most likely sequence for every read. We,
 instead, use a greedy scheme that can be seen as an approximation to
 PyroNoise. According to several test data sets, the approximation gives
 very similar results in a fraction of the time.

Depends: mothur
Homepage: http://www.mothur.org
License: free
WNPP: 589675
Responsible: Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de>
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mothur/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mothur/trunk/
Pkg-Description: sequence analysis for research on microbiota
 Mothur seeks to develop a single piece of open-source, expandable
 software to fill the bioinformatics needs of the microbial ecology
 community. It has incorporated the functionality of dotur, sons,
 treeclimber, s-libshuff, unifrac, and much more. In addition to improving
 the flexibility of these algorithms, a number of other features including
 calculators and visualization tools were added.

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.


Comment: Several related R packages are listed at CRAN:
         http://cran.r-project.org/web/views/Genetics.html