[Blends-commit] r3123 - /projects/debug/tasks/bio
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Thu Jan 26 22:07:52 UTC 2012
Author: tille
Date: Thu Jan 26 22:07:52 2012
New Revision: 3123
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3123
Log:
bisecting problematic task
Modified:
projects/debug/tasks/bio
Modified: projects/debug/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/debug/tasks/bio?rev=3123&op=diff
==============================================================================
--- projects/debug/tasks/bio (original)
+++ projects/debug/tasks/bio Thu Jan 26 22:07:52 2012
@@ -2,1490 +2,6 @@
Description: Debian Med micro-biology packages
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
-
-X-Begin-Category: Phylogenetic analysis
-
-Depends: altree
-Remark: altree 1.1.0 should be not be packaged
- According to Vincent Danjean <vdanjean.ml at free.fr> version 1.1.0 should not
- be packaged for two reasons:
- .
- 1. New dependencies (libtamuanova-perl, nanova and libnanova-perl) which
- need to be packaged.
- 2. There are still bugs in the new method added in altree 1.1.0 and the doc
- is not updated.
- .
- See http://lists.debian.org/debian-med/2009/08/msg00104.html for further
- details.
-
-Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle
-
-Depends: probalign
-
-Depends: treeviewx
-X-Published-Authors: FIXME
-X-Published-Title: FIXME
-Published-In: Computer Applications in the Bioscience 12:357-358
-Published-Year: 1996
-
-Depends: figtree
-
-X-End-Category: Phylogenetic analysis
-
-Depends: molphy, phylip
-Why: Phylogenetic analysis (Non-free, thus only suggested).
-
-X-Comment: treetool is removed from Debian because it is not maintained upstream since
- 1995 and cause the Xserver to freeze under Squeeze
-
-Depends: fastlink, loki, plink, r-cran-qtl
-Why: Genetics
-
-X-Begin-Category: Sequence alignments and related programs.
-
-Depends: amap-align
-Remark: Dead upstream
- The homepage of this project vanished as well as the Download area. An
- old unmaintained version remained at code.google.com. Please drop the
- maintainer a note if you have any news of this project.
-
-Depends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, wise
-
-Depends: maqview
-
-Depends: bwa
-Published-Title: Fast and accurate short read alignment with Burrows-Wheeler transform
-Published-Authors: Li, Heng and Durbin, Richard
-Published-In: Bioinformatics 25(14):1754-1760
-Published-Year: 2009
-Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754
-
-Depends: mummer
-Published-Title: Versatile and open software for comparing large genomes
-Published-Authors: Stefan Kurtz, Adam Phillippy, Arthur L. Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L. Salzberg
-Published-In: Genome Biol. 5(2):R12
-Published-Year: 2004
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/14759262
-Published-DOI: 10.1186/gb-2004-5-2-r12
-Published-PubMed: 14759262
-
-Depends: blast2
-Published-Title: Basic local alignment search tool
-Published-Authors: S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman
-Published-In: J Mol Biol. 215(3):403-410
-Published-Year: 1990
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/2231712
-
-Depends: mafft
-Published-Title: Multiple alignment of DNA sequences with MAFFT
-Published-Authors: K. Katoh, G. Asimenos, H. Toh
-Published-In: Methods Mol Biol. 537:39-64
-Published-Year: 2009
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19378139
-Published-PubMed: 19378139
-
-Depends: t-coffee
-Published-Title: T-Coffee: A novel method for multiple sequence alignments
-Published-Authors: C. Notredame, D. Higgins, J. Heringa
-Published-In: Journal of Molecular Biology 302(1):205-217
-Published-Year: 2000
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
-Published-PubMed: 10964570
-Remark: Do not update to version 9.0
- Version 9.0 contains non-free code. See http://bugs.debian.org/649263.
-
-Depends: kalign
-Published-Title: Kalign--an accurate and fast multiple sequence alignment algorithm
-Published-Authors: Lassmann T, Sonnhammer EL.
-Published-In: BMC Bioinformatics, 6:298
-Published-Year: 2005
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16343337
-Published-PubMed: 16343337
-
-Depends: hmmer
-Published-Title: Multiple Alignment Using Hidden Markov Models.
-Published-Authors: S. R. Eddy.
-Published-In: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology, 114-120.
-Published-Year: 1995
-Published-URL: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf
-
-Depends: exonerate
-Published-Title: Automated generation of heuristics for biological sequence comparison
-Published-Authors: G.C. Slater, E. Birney
-Published-In: BMC Bioinformatics 6:31
-Published-Year: 2005
-Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
-Published-doi: 10.1186/1471-2105-6-31
-
-Depends: dialign
-Published-Authors: Burkhard Morgenstern
-Published-Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
-Published-In: Bioinformatics 15(3):211-218
-Published-Year: 1999
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10222408
-
-Depends: dialign-tx
-Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
-Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
-Published-In: Algorithms for Molecular Biology 3:6
-Published-Year: 2008
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568
-
-Depends: poa
-Published-Authors: C. Grasso, C. Lee
-Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
-Published-In: Bioinformatics 20(10):1546-1556.
-Published-Year: 2004
-
-Depends: probcons
-Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
-Published-In: Genome Research 15: 330-340
-Published-Year: 2005
-
-Depends: proda
-Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
-Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
-Published-In: Nucleic Acids Research 34(20), 5932-5942
-Published-Year: 2006
-
-Depends: seaview
-Published-Authors: N. Galtier, M. Gouy, C. Gautier
-Published-Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny
-Published-In: Comput. Applic. Biosci. 12:543-548
-Published-Year: 1996
-
-Depends: sigma-align
-X-Published-Authors: FIXME
-X-Published-Title: FIXME
-Published-In: BMC Bioinformatics 16;7:143
-Published-Year: 2006
-
-Depends: emboss
-Published-Authors: P. Rice, I. Longden, A. Bleasby
-Published-Title: EMBOSS: the European Molecular Biology Open Software Suite.
-Published-In: Trends Genet., 16(6):276-277
-Published-Year: 2000
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10827456
-
-Depends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
-Suggests: emboss-explorer
-Why: The EMBOSS sequence analysis suite and its galaxy.
-
-Depends: arb
-Why: Sequence alignments and related programs (Non-free, thus only suggested).
-
-Depends: clustalx, clustalo
-
-Depends: clustalw
-Published-Authors: M. Larkin, et al.
-Published-Title: Clustal W and Clustal X version 2.0
-Published-In: Bioinformatics 23(21):2947-2948
-Published-Year: 2007
-
-Depends: clustalw-mpi
-Comment: Originally the dependency was clustalw | clustalw-mpi but currently it is
- not possible to specify an "OR relation" and tag the Published-* fields to only one
- of them.
-
-Depends: mothur, bowtie, dotur
-
-Depends: transtermhp
-
-X-End-Category: Sequence alignments and related programs.
-
-X-Begin-Category: high-throughput sequencing
-
-Depends: last-align, maq, ssake, velvet
-
-Depends: qiime
-
-X-End-Category: high-throughput sequencing
-
-X-Begin-Category: Analysis of RNA sequences.
-
-Depends: infernal
-Published-Authors: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
-Published-Title: Infernal 1.0: inference of RNA alignments
-Published-In: Bioinformatics 15;25(10):1335-7
-Published-Year: 2009
-Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/full/25/10/1335
-
-Depends: rnahybrid
-Published-Authors: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann, Robert Giegerich
-Published-Title: Fast and effective prediction of microRNA/target duplexes RNA
-Published-In: 10:1507-1517
-Published-Year: 2004
-X-Category: Target duplex prediction
-
-X-End-Category: Analysis of RNA sequences.
-
-X-Begin-Category: Molecular modelling and molecular dynamics
-
-Depends: adun.app
-Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator
-Published-Authors: M.A. Johnston, I.F. Galván, J. Villà -Freixa
-Published-In: J. Comp. Chem
-Published-Year: 2005
-Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT
-Published-DOI: 10.1002/jcc.20312
-
-Depends: garlic, gamgi, gdpc, ghemical, jmol, pymol, r-other-bio3d, massxpert
-Comment: r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team
-
-Depends: gromacs
-Published-Title: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-Published-Authors: B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl
-Published-In: J. Chem. Theory Comput.
-Published-Year: 2008
-Published-URL: http://pubs.acs.org/doi/abs/10.1021/ct700301q
-Published-DOI: 10.1021/ct700301q
-X-Published-Other: Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis. J Mol Model. 2001;7(8):306.17.
-X-Published-Other: Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: Fast, Flexible, and Free. J Comput Chem. 2005;26(16):1701.18. [PubMed]
-
-Depends: rasmol
-Registration: http://www.rasmol.org/register.shtml
-Published-Title: RasMol: Biomolecular graphics for all
-Published-Authors: Roger Sayle and E. James Milner-White
-Published-In: Trends in Biochemical Sciences (TIBS)
-Published-Year: 1995
-
-X-End-Category: Molecular modelling and molecular dynamics
-
-Depends: plasmidomics
-Why: Presentation
-
-X-Begin-Category: Tools for the molecular biologist.
-
-Depends: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer
-
-Depends: melting
-Published-Authors: Nicolas Le Novère
-Published-Title: MELTING, computing the melting temperature of nucleic acid duplex
-Published-In: Bioinformatics, 17: S.1226-1227
-Published-Year: 2001
-
-Suggests: melting-gui
-Comment: I think it makes sense to point users to GUI applications as well as to
- the console applications - in this case melting (Andreas Tille)
-
-Depends: mipe
-Published-Authors: Aerts J & Veenendaal T.
-Published-Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
-Published-In: Online Journal of Bioinformatics 6(2): 114-120
-Published-Year: 2005
-
-Depends: primer3
-Published-Authors: S. Rozen, H. Skaletsky
-Published-Title: Primer3 on the WWW for general users and for biologist programmers
-Published-In: Methods Mol Biol. 132:365-86
-Published-Year: 2000
-
-X-End-Category: Tools for the molecular biologist.
-
-X-Begin-Category: Genome Browser
-
-Depends: gbrowse
-X-Importance: Academic ones are really expensive for commercial use
-
-X-End-Category: Genome Browser
-
-Depends: biomaj
-
-Suggests: mozilla-biofox
-Why: Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
-
-Depends: glam2
-Why: Motif search
-Published-Title: Discovering sequence motifs with arbitrary insertions and deletions
-Published-Authors: MC Frith, NFW Saunders, B Kobe, TL Bailey
-Published-In: PLoS Computational Biology
-Published-Year: 2008
-Published-DOI: 10.1371/journal.pcbi.1000071
-
-Depends: raster3d
-
-Depends: phyml
-
-Depends: autodock
-Registration: http://autodock.scripps.edu/downloads/autodock-registration
-Why: Molecular modelling and molecular dynamics.
-Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-Published-Authors: G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson
-Published-In: J. Comput. Chem.
-Published-Year: 2009
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
-Published-Pubmed: 19399780
-Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
-Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
-Published-In: Nucleic Acids Research 34(20), 5932-5942
-Published-Year: 2006
-
-Depends: autogrid
-
-Depends: autodock-vina
-
-Depends: autodocktools
-Comment: The package autodocktools depends from the mgltools-* packages mentioned
- above, so they will be installed even if they would not be mentioned in
- the list of Depends in the metapackage med-bio. But leaving them out here
- would hide them from the tasks and bugs list as well from the sectioning in
- http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3
- so they are mentioned here in addition to autodocktools.
- .
- This was changed by adding Enhances field to the packages in question.
-Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-Published-Authors: G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson
-Published-In: J. Comput. Chem.
-Published-Year: 2009
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
-
-Depends: mustang
-Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
-Published-Title: MUSTANG: A multiple structural alignment algorithm
-Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
-Published-Year: 2006
-
-Depends: theseus
-
-Depends: staden-io-lib-utils
-
-Depends: samtools, bedtools, filo
-
-Depends: gassst
-
-Depends: macs
-
-Depends: r-bioc-hilbertvis
-Published-Authors: Simon Anders
-Published-Title: Visualization of genomic data with the Hilbert curve
-Published-In: Bioinformatics 25(10):1231-1235
-Published-Year: 2009
-Published-DOI: 10.1093/bioinformatics/btp152
-Remark: It would be interesting to package HilbertVisGUI (see below) as well.
-
-Depends: r-other-mott-happy
-Published-Authors: Richard Mott, Christopher J. Talbot, Maria G. Turri, Allan C. Collins, Jonathan Flint
-Published-Title: A method for fine mapping quantitative trait loci in outbred animal stocks
-Published-In: Proc. Natl. Acad. Sci. USA
-Published-Year: 2000
-Published-DOI: 10.1073/pnas.230304397
-Remark: Do not upgrade this package
- Steffen Möller is scientifically collaborating with upstream and nothing shall
- happen to that package until authors give their confirmation.
-
-Depends: seq-gen
-
-Depends: mira-assembler
-Published-Title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
-Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.
-Published-In: Genome Res. Jun;14(6):1147-59.
-Published-Year: 2004
-Published-doi: 10.1101/gr.1917404
-Published-URL: http://pubmed.org/15140833
-
-Depends: bagphenotype
-Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
-License: GPL-3
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bagphenotype/bagphenotype/trunk/
-Pkg-Description: CLI for the bagphenotype R package
- mapping QTLs in populations descended from known founders
-
-Depends: r-other-valdar-bagphenotype.library
-Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
-License: GPL-3
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-other-valdar-bagphenotype/trunk/
-Pkg-Description: GNU R extension of the functionality of happy
- mapping QTLs in populations descended from known founders
-
-Depends: alien-hunter
-Published-Title: Interpolated variable order motifs for identification of horizontally acquired DNA:
- revisiting the Salmonella pathogenicity islands
-Published-Authors: GS Vernikos and J. Parkhill
-Published-In: Bioinformatics
-Published-Year: 2006
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16837528
-Published-DOI: 10.1093/bioinformatics/btl369
-Published-PubMed: 16837528
-
-Suggests: seqan-apps
-
-Depends: ncoils
-
-Depends: gentle
-
-Depends: gmap
-Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences
-Published-Authors: Thomas D. Wu, Colin K. Watanabe
-Published-In: Bioinformatics
-Published-Year: 2005
-Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859
-
-Depends: igv
-
-Depends: picard-tools
-
-Depends: acedb-other-dotter, acedb-other-belvu, acedb-other
-
-Depends: python-cogent
-
-Depends: paml
-
-Depends: ensembl
-
-Depends: mrbayes
-
-Suggests: pdb2pqr
-
-Depends: squizz
-
-Depends: clonalframe
-
-Depends: jellyfish
-Published-Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-Published-Authors: Guillaume Marcais and Carl Kingsford
-Published-In: Bioinformatics
-Published-Year: 2011
-Published-DOI: 10.1093/bioinformatics/btr011
-
-Depends: r-other-genabel
-Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
-Responsible: Steffen Moeller <steffen_moeller at gmx.de>
-License: GPL 2+
-WNPP: 492044
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-other-genabel/trunk/
-Pkg-Description: genome-wide SNP association analysis
- A package for genome-wide association analysis between quantitative
- or binary traits and single-nucleiotide polymorphisms (SNPs).
-
-Depends: meme
-Homepage: http://meme.nbcr.net/meme/
-Responsible: Steffen Moeller <moeller at debian.org>
-License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/meme/trunk/
-Pkg-Description: motif discovery and search
- MEME is a tool for discovering motifs in a group of related DNA or protein
- sequences. A motif is a sequence pattern that occurs repeatedly in a group
- of related protein or DNA sequences. MEME represents motifs as position-dependent
- letter-probability matrices which describe the probability of each possible
- letter at each position in the pattern. Individual MEME motifs do not contain
- gaps. Patterns with variable-length gaps are split by MEME into two or more
- separate motifs.
- .
- MEME takes as input a group of DNA or protein sequences (the training set)
- and outputs as many motifs as requested. MEME uses statistical modeling
- techniques to automatically choose the best width, number of occurrences,
- and description for each motif.
-
-Depends: vienna-rna
-Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
-Responsible: Alex Mestiashvili <alex at biotec.tu-dresden.de>
-License: non-free but redistributable
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/vienna-rna/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/vienna-rna/trunk/
-WNPP: 451193
-X-Category: Secondary structure of nucleic acids
-Pkg-Description: RNA sequence analysis
- The Vienna RNA Package consists of a C code library and several
- stand-alone programs for the prediction and comparison of RNA secondary
- structures.
-
-Depends: cytoscape
-Homepage: http://cytoscape.org/
-Responsible: Mike Smoot <mes at aescon.com>
-License: LGPL
-WNPP: 465331
-Pkg-Description: visualizing molecular interaction networks
- Cytoscape is a bioinformatics software platform for visualizing molecular
- interaction networks and integrating these interactions with gene expression
- profiles and other state data. Additional features are available as plugins.
-
-Depends: ballview
-Published-Title: BALLView: a tool for research and education in molecular modeling.
-Published-Authors: A. Moll, A. Hildebrandt, H.P.Lenhof, O. Kohlbacher
-Published-In: Bioinformatics, 22(3):365-6
-Published-Year: 2006
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16332707
-
-Depends: python-pynast
-Published-Title: PyNAST: a flexible tool for aligning sequences to a template alignment
-Published-Authors: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
-Published-In: Bioinformatics 26: 266-267
-Published-Year: 2010
-Published-DOI: 10.1093/bioinformatics/btp636
-
-Depends: raxml
-
-Depends: mlv-smile
-
-Depends: axparafit
-Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
-Responsible: David Paleino <d.paleino at gmail.com>
-License: GPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/axparafit/trunk/
-WNPP: 464323
-Pkg-Description: optimized statistical analysis of host-parasite coevolution
- AxParafit is a highly optimized version of Pierre Legendre's Parafit
- program for statistical analysis of host-parasite coevolution.
- AxParafit has been parallelized with MPI (Message Passing Interface)
- for compute clusters and was used to carry out the largest
- co-evolutionary analysis to date for the paper describing the software.
-
-Depends: axpcoords
-Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
-Responsible: David Paleino <d.paleino at gmail.com>
-License: GPL
-WNPP: 464323
-Pkg-Description: LAPACK-based implementation of DistPCoA
- AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
- http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
- which is another program by Pierre Legendre, it conducts a principal
- coordinates analysis.
- This program is required for the pipeline that conducts a full host-parasite
- co-phylogenetic analysis in combination with AxParafit.
-
-Depends: copycat
-Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
-License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
-Pkg-Description: fast access to cophylogenetic analyses
- CopyCat provides an easy and fast access to cophylogenetic analyses.
- It incorporates a wrapper for the program ParaFit, which conducts a
- statistical test for the presence of congruence between host and
- parasite phylogenies. CopyCat offers various features, such as the
- creation of customized host-parasite association data and the
- computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
-
-Depends: btk-core
-Homepage: http://sourceforge.net/projects/btk/
-Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
-License: GPL
-WNPP: 459753
-Pkg-Description: biomolecule Toolkit C++ library
- The Biomolecule Toolkit is a library for modeling biological
- macromolecules such as proteins, DNA and RNA. It provides a C++ interface
- for common tasks in structural biology to facilitate the development of
- molecular modeling, design and analysis tools.
-
-Depends: tacg
-Homepage: http://sourceforge.net/projects/tacg
-Responsible: Charles Plessy <plessy at debian.org>
-License: GPL and others
-WNPP: 461504
-X-Category: Motif detection
-X-Importance: powerful
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/tacg/trunk/
-Pkg-Description: command line program for finding patterns in nucleic acids
- tacg is a character-based, command line tool for unix-like operating systems
- for pattern-matching in nucleic acids and performing some of the basic protein
- manipulations. It was originally designed for restriction enzyme analysis of
- DNA, but has been extended to other types of matching. It now handles
- degenerate sequence input in a variety of matching approaches, as well as
- patterns with errors, regular expressions and TRANSFAC-formatted matrices.
- .
- It was designed to be a grep for DNA and like the original grep, its
- capabilities have grown so that now the author has to keep calling up the help
- page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
- application in any sense. However, it's existance as a strictly command-line
- tool lends itself well to Webification and wrapping by various GUI tools and
- it is now distributed with a web interface form and a Perl CGI handler.
- Additionally, it can easily be integrated into editors that support shell
- commands such as nedit.
- .
- The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
- BMC Bioinformatics. 3:8 http://www.biomedcentral.com/1471-2105/3/8
-
-Depends: treeplot
-Responsible: Charles Plessy <plessy at debian.org>
-License: GPL
-WNPP: 461508
-X-Category: Phylogenetic analysis
-X-Importance: Tree export to graphical formats
-Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treeplot
-Pkg-Description: Phylogenetic tree file converter
- Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to
- Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic
- (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language
- (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map
- file (.pnm)
- .
- The upstream author Olivier Langella says: 'I think that "treeplot"
- is outdated. "Treeviewx" is an equivalent that works great and it is
- already packaged. ... you can replace "treeplot" with
- "populations". I would be pleased if "populations" became a Debian
- package.' So this package should probably be delisted in favour of
- populations (see http://lists.debian.org/debian-med/2008/03/msg00124.html).
-
-Depends: treevolve
-Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
-Responsible: Charles Plessy <plessy at debian.org>
-License: has to be verified
-WNPP: 461510
-Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treevolve
-Pkg-Description: simulation of evolution of DNA sequences
- treevolve will simulate the evolution of DNA sequences under a
- coalescent model, which allows exponential population growth,
- population subdivision according to an island model, migration and
- recombination. In addition different periods of population dynamics
- can be enforced at different times. For example, a period of
- exponential growth can be followed by a period of stasis where the
- population is subdivided into demes. Multiple sets of such simulated
- sequence data can then be compared to sequence data sampled from a
- population of interest using suitable statistics, and various
- evolutionary hypotheses concerning the evolution of this population
- tested.
- .
- Citation: Population dynamics of HIV-1 inferred from gene sequences
- Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
-
-Depends: asap
-Homepage: http://asap.ahabs.wisc.edu/software/asap/
-Responsible: Andreas Tille <tille at debian.org>
-License: GPL
-Pkg-Description: organize the data associated with a genome
- Developments in genome-wide approaches to biological research have
- yielded greatly increased quantities of data, necessitating the cooperation
- of communities of scientists focusing on shared sets of data. ASAP
- leverages the internet and database technologies to meet these needs.
- ASAP is designed to organize the data associated with a genome from the
- early stages of sequence annotation through genetic and biochemical
- characterization, providing a vehicle for ongoing updates of the annotation
- and a repository for genome-scale experimental data. Development was
- motivated by the need to more directly involve a greater community of
- researchers, with their collective expertise, in keeping the genome
- annotation current and to provide a synergistic link between up-to-date
- annotation and functional genomic data. The system is continually under
- development at the Genome Evolution Lab with the stable, in-use, publicly
- available University of Wisconsin installation updated regularly.
- .
- Software development on ASAP began in early 2002, and ASAP has been
- continually improved up until the present day. A longstanding goal of
- the ASAP project was to make the source code of ASAP available so that
- other installations of ASAP could be implemented. As future ASAP
- installations come to pass, ASAP will be further extended to be
- inter-operable between sites.
-X-Category: Annotation
-
-Depends: emboss-kaptain
-Homepage: http://userpage.fu-berlin.de/~sgmd/download.html
-Responsible: Charles Plessy <plessy at debian.org>
-License: GPL-2+
-WNPP: 466682
-Pkg-Description: graphical interface to EMBOSS using Kaptain
- EMBOSS.kaptn is a graphical user interface (GUI) for more than 200
- programms of the EMBOSS sequence analysis package. It uses Kaptain, a
- universal front-end for command line applications. EMBOSS is a
- collection of high-quality free Open Source software for sequence
- analysis. With EMBOSS.kaptn it integrates nicely into X window based
- desktops like KDE.
-
-Depends: agdbnet
-Homepage: http://pubmlst.org/software/database/agdbnet/
-Responsible: Andreas Tille <tille at debian.org>
-License: GPL
-WNPP: 500106
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/agdbnet/trunk/
-Pkg-Description: antigen sequence database software for web-based bacterial typing
- AgdbNet is antigen sequence database software for web-based bacterial
- typing. The software facilitates simultaneous BLAST querying of multiple
- loci using either nucleotide or peptide sequences. It's written in Perl
- and runs on Linux/UNIX systems.
- .
- Databases are described by XML files and can have any number of loci, which
- may be defined by nucleotide and/or peptide sequences. The databases can
- optionally have integral isolate tables so that information about representative
- isolates can be retrieved or they may be configured to query external isolate
- databases, such as those hosted on PubMLST.org.
- .
- The software is used on a number of public bacterial typing databases:
- * Neisseria PorA variable regions | PorB | FetA
- * Campylobacter flaA
- * Streptococcus equi seM
-
-Depends: martj
-Homepage: http://www.ebi.ac.uk/biomart/
-Responsible: Steffen Moeller <moeller at debian.org>
-License: GPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/martj/trunk/
-Pkg-Description: distributed data integration system for biological data
- BioMart is a simple, distributed data integration system with
- powerful query capabilities. The BioMart data model has been applied
- to the following data sources: UniProt Proteomes, Macromolecular
- Structure Database (MSD), Ensembl, Vega, and dbSNP.
-
-Depends: cluster3
-Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
-License: non-free
-WNPP: 286167
-Responsible: Steffen Moeller <moeller at debian.org>
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cluster3/trunk/
-Pkg-Description: find clustering solutions for genome data
- Cluster 3.0 is an enhanced version of Cluster, which was originally
- developed by Michael Eisen while at Stanford University. The main
- improvement consists of the k-means algorithm, which now includes
- multiple trials to find the best clustering solution. This is crucial
- for the k-means algorithm to be reliable. The routine for self-organizing
- maps was extended to include 2D rectangular geometries. The Euclidean
- distance and the city-block distance were added to the available
- measures of similarity.
-
-Depends: jtreeview
-Homepage: http://jtreeview.sourceforge.net/
-Responsible: Steffen Moeller <moeller at debian.org>
-License: GPL
-WNPP: 243771
-X-Category: Visualisation
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/treeview/trunk/
-Pkg-Description: Java re-implementation of Michael Eisen's TreeView
- TreeView creates a matrix-like display of expression data, known as
- Eisen clustering. The original implementation was a Windows program
- named TreeView by Michael Eisen. This TreeView package, sometimes also
- referred to as jTreeView, was rewritten in Java under a free license,
- the original implementation also comes with the source code, but controls
- commercial distribution. And it did not run on Unix.
- .
- Java TreeView is an extensible viewer for microarray data in
- PCL or CDT format.
-
-Depends: cactus
-Homepage: http://www.cactuscode.org/Community/Biology.html
-License: GPL
-Pkg-Description:
- Cactus is an open source problem solving environment designed for scientists
- and engineers. Its modular structure easily enables parallel computation
- across different architectures and collaborative code development between
- different groups.
- .
- Cactus provides easy access to many cutting edge software technologies being
- developed in the academic research community, including the Globus
- Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
- adaptive mesh refinement, web interfaces, and advanced visualization tools.
-
-Depends: contralign
-Homepage: http://contra.stanford.edu/contralign/
-License: Public Domain
-Pkg-Description: parameter learning framework for protein pairwise sequence alignment
- CONTRAlign is an extensible and fully automatic parameter learning
- framework for protein pairwise sequence alignment based on pair
- conditional random fields. The CONTRAlign framework enables the
- development of feature-rich alignment models which generalize well to
- previously unseen sequences and avoid overfitting by controlling model
- complexity through regularization.
-
-Depends: galaxy
-Homepage: http://g2.trac.bx.psu.edu/
-License: MIT
-WNPP: 432472
-Pkg-Description: manipulate sequences and annotation files
- Galaxy is a web-based tool allowing users to perform operations which
- are usually done with command-line interface. Using galaxy, one can
- manipulate sequences and annotation files in many formats. Galaxy has
- strong ties with the UCSC genome browser, and makes it easy to
- visualise modified annotation files as a custom track.
-
-Depends: genographer
-Homepage: http://hordeum.oscs.montana.edu/genographer/
-License: GPL
-Pkg-Description: read data and reconstruct them into a gel image
- This program will read in data from an ABI 3700, 3100, 377 or 373,
- CEQ 2000 or SCF and reconstruct them into a gel image which is
- straightened and sized. Bins can be defined easily and viewed as
- thumbnails, which allows for a fairly quick and easy way of scoring a gel.
- .
- The program is written in Java and uses the Java 1.3 API. Therefore,
- it should run on any machine that can run java.
-
-Depends: molekel
-Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
-License: GPL
-Pkg-Description: multiplatform molecular visualization
- Molekel is an opensource (GPL) multiplatform molecular visualization
- program being developed at the Swiss National Supercomputing Centre
- (CSCS).
-
-Depends: pftools
-Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
-License: GPL
-Pkg-Description: tools to handle patterns from PROSITE
- ps_scan is a perl program used to scan one or several patterns, rules
- and/or profiles from PROSITE against one or several protein sequences
- in Swiss-Prot or FASTA format. It requires two compiled external
- programs from the PFTOOLS, which are also distributed with the sources.
-
-Depends: proalign
-Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
-License: GPL
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 378290
-Pkg-Description: Probabilistic multiple alignment program
- ProAlign performs probabilistic sequence alignments using hidden Markov
- models (HMM). It includes a graphical interface (GUI) allowing to (i)
- perform alignments of nucleotide or amino-acid sequences, (ii) view the
- quality of solutions, (iii) filter the unreliable alignment regions and
- (iv) export alignments to other softwares.
- .
- ProAlign uses a progressive method, such that multiple alignment is
- created stepwise by performing pairwise alignments in the nodes of a
- guide tree. Sequences are described with vectors of character
- probabilities, and each pairwise alignment reconstructs the ancestral
- (parent) sequence by computing the probabilities of different
- characters according to an evolutionary model. It has been published in
- Bioinformatics. 2003 Aug 12;19(12):1505-13.
-
-Depends: ssaha
-Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
-License: GPL
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 425111
-Pkg-Description: Sequence Search and Alignment by Hashing Algorithm
- SSAHA is a software tool for very fast matching and alignment of DNA
- sequences. It achieves its fast search speed by converting sequence
- information into a `hash table' data structure, which can then be
- searched very rapidly for matches. It was published by Ning Z,
- Cox AJ, Mullikin JC in Genome Res. 2001;11;1725-9.
- .
- SSAHA is the only free software of its category (fast search of nearly
- indentical sequences). The popular alternative, BLAT, is restricted to
- non-commercial use.
- .
- Unfortunately the source of its successor ssaha2
- http://www.sanger.ac.uk/Software/analysis/SSAHA2/
- can not be relieased as Open Source because it contains
- proprietary code.
-Remark: Successor for ssaha2 available: smalt
- The program smalt is from the same author is according to its author
- faster and more precise than ssaha2 (except for sequences > 2000bp)
-
-Depends: ngila
-Homepage: http://scit.us/projects/ngila/
-License: GPLv3
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 439996
-Pkg-Description: global pairwise alignments with logarithmic and affine gap costs
- Ngila is an application that will find the best alignment of a pair
- of sequences using log-affine gap costs, which are the most
- biologically realistic gap costs.
- .
- Ngila implements the Miller and Myers (1988) algorithm in order to
- find a least costly global alignment of two sequences given homology
- costs and a gap cost. Two versions of the algorithm are
- included: holistic and divide-and-conquer. The former is faster but
- the latter utilizes less memory. Ngila starts with the
- divide-and-conquer method but switches to the holistic method for
- subsequences smaller than a user-established threshold. This improves
- its speed without substantially increasing memory requirements. Ngila
- also allows users to assign costs to end gaps that are smaller than
- costs for internal gaps. This is important for aligning using the
- free-end-gap method.
- .
- Ngila is published in Cartwright RA Bioinformatics 2007
- 23(11):1427-1428; doi:10.1093/bioinformatics/btm095
-
-Depends: tm-align
-
-Depends: dazzle
-Homepage: http://www.biojava.org/dazzle
-Responsible: Steffen Moeller <moeller at debian.org>
-License: LGPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/dazzle/trunk/
-Pkg-Description: Java-based DAS server
- Dazzle is a general purpose server for the Distributed Annotation System
- (DAS) protocol. It is implemented as a Java servlet, using the BioJava
- APIs. Dazzle is a modular system which uses small "datasource" plugins to
- provide access to a range of databases. Several general-purpose plugins
- are included in the package, and it it straightforward to develop new
- plugins to connect to your own databases.
- .
- Information on DAS is available from http://www.biodas.org/
-
-Depends: ecell
-Homepage: http://www.e-cell.org/
-Responsible: Steffen Moeller <moeller at debian.org>
-WNPP: 241195
-License: GPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ecell/trunk/
-Pkg-Description: Concept and environment for constructing virtual cells on computers
- The E-Cell Project is an international research project aiming at
- developing necessary theoretical supports, technologies and software
- platforms to allow precise whole cell simulation.
- .
- The E-Cell System is an object-oriented software suite for modeling,
- simulation, and analysis of large scale complex systems such as
- biological cells, architected by Kouichi Takahashi and written by
- a team of developers.
- .
- The core part of the system, E-Cell Simulation Environment version 3,
- allows many components driven by multiple algorithms with different
- timescales to coexist.
- .
- E-Cell System consists of the following three major parts:
- * E-Cell Simulation Environment (or E-Cell SE)
- * E-Cell Modeling Environment (or E-Cell ME)
- * E-Cell Analysis Toolkit.
-
-Depends: haploview
-Homepage: http://www.broad.mit.edu/mpg/haploview/
-Responsible: Steffen Moeller <moeller at debian.org>
-WNPP: 311421
-License: DFSG free
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/haploview/trunk/
-Pkg-Description: Analysis and visualization of LD and haplotype maps
- This tools assists in the analysis of the nucleotide
- variation in a population. Such investigations are performed
- to determine genes and genetic pathways that are associated
- with diseases. This is an early stage in the quest for new drugs.
-
-Depends: bio-mauve
-Homepage: http://asap.ahabs.wisc.edu/mauve/
-Responsible: Andreas Tille <tille at debian.org>
-License: GPL
-Language: C++ and Java
-X-Category: Multiple genome alignment
-X-Importance: efficient
-Pkg-Description: multiple genome alignment
- Mauve is a system for efficiently constructing multiple genome alignments
- in the presence of large-scale evolutionary events such as rearrangement
- and inversion. Multiple genome alignment provides a basis for research
- into comparative genomics and the study of evolutionary dynamics. Aligning
- whole genomes is a fundamentally different problem than aligning short
- sequences.
- .
- Mauve has been developed with the idea that a multiple genome aligner
- should require only modest computational resources. It employs algorithmic
- techniques that scale well in the amount of sequence being aligned. For
- example, a pair of Y. pestis genomes can be aligned in under a minute,
- while a group of 9 divergent Enterobacterial genomes can be aligned in
- a few hours.
- .
- Mauve computes and interactively visualizes genome sequence comparisons.
- Using FastA or GenBank sequence data, Mauve constructs multiple genome
- alignments that identify large-scale rearrangement, gene gain, gene loss,
- indels, and nucleotide substutition.
- .
- Mauve is developed at the University of Wisconsin.
- .
- Note: There are instructions for compiling Mauve from source available at
- http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html
-
-Depends: mauvealigner
-Homepage: http://asap.ahabs.wisc.edu/mauve/
-Responsible: Andreas Tille <tille at debian.org>
-License: GPL
-Pkg-URL: http://people.debian.org/~tille/packages/mauvealigner/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mauvealign/trunk/
-Pkg-Description: multiple genome alignment algorithms
- The mauveAligner and progressiveMauve alignment algorithms have been
- implemented as command-line programs included with the downloadable Mauve
- software. When run from the command-line, these programs provide options
- not yet available in the graphical interface.
- .
- Mauve is a system for efficiently constructing multiple genome alignments
- in the presence of large-scale evolutionary events such as rearrangement
- and inversion. Multiple genome alignment provides a basis for research
- into comparative genomics and the study of evolutionary dynamics. Aligning
- whole genomes is a fundamentally different problem than aligning short
- sequences.
- .
- Mauve has been developed with the idea that a multiple genome aligner
- should require only modest computational resources. It employs algorithmic
- techniques that scale well in the amount of sequence being aligned. For
- example, a pair of Y. pestis genomes can be aligned in under a minute,
- while a group of 9 divergent Enterobacterial genomes can be aligned in
- a few hours.
- .
- Mauve computes and interactively visualizes genome sequence comparisons.
- Using FastA or GenBank sequence data, Mauve constructs multiple genome
- alignments that identify large-scale rearrangement, gene gain, gene loss,
- indels, and nucleotide substutition.
- .
- Mauve is developed at the University of Wisconsin.
-
-Depends: phylographer
-Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
-License: GPL
-X-Category: Graphical representation of sequence conservation
-Language: Tcl/Tk
-Pkg-Description: Graph Visualization Tool
- PhyloGrapher is a program designed to visualize and study evolutionary
- relationships within families of homologous genes or proteins
- (elements). PhyloGrapher is a drawing tool that generates custom graphs
- for a given set of elements. In general, it is possible to use
- PhyloGrapher to visualize any type of relations between elements.
- Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
- the results of a BLAST search as a graph.
- .
- PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
- biological sequence alignment reports (BLAST is provided by Debian's
- blast2 package).
-Remark: Outdated upstream, better alternatives available
- The former packaging effort of this package was dropped. It seems
- that http://cytoscape.org/ is a reasonable replacement.
-
-Depends: phylowin
-Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
-WNPP: 395840
-License: unknown
-Pkg-Description: Graphical interface for molecular phylogenetic inference
- Phylo_win is a graphical colour interface for molecular phylogenetic
- inference. It performs neighbor-joining, parsimony and maximum
- likelihood methods and bootstrap with any of them. Many distances can be
- used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
- (1995), LogDet for nucleotidic sequences, Poisson correction for protein
- sequences, Ka and Ks for codon sequences. Species and sites to include
- in the analysis are selected by mouse. Reconstructed trees can be drawn,
- edited, printed, stored and evaluated according to numerous criteria.
- .
- This program uses sources files from the Phylip program, which forbids
- its use for profit. Therfore, Phylo_win will unfortunately have to be
- distributed in contrib or non-free.
-Remark: Issuer of previous ITP said:
- Because I could never figure out the license of Phylo_win, and because the
- upstream authors released SeaView 4, which provides similar functionalities, I
- will not package Phylo_win.
- .
- Probably it makes sense to remove this project from the prospective packages
- list.
-
-Depends: wgs-assembler
-Homepage: http://wgs-assembler.sourceforge.net/
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 395843
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wgs-assembler/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/wgs-assembler/trunk/
-License: GPL
-Pkg-Description: Whole-Genome Shotgun Assembler
- Celera Assembler is scientific software for DNA research. It can
- reconstruct long sequences of genomic DNA given the fragmentary data
- produced by whole-genome shotgun sequencing. The Celera Assembler
- enabled many advances in genomics, including the first genome
- sequence of a multi-cellular organism and the first diploid sequence
- of an individual human.
- .
- The Celera Assembler is a member of a class of software called
- whole-genome shotgun assemblers. The Celera Assembler is mature,
- efficient, open-source software with a long record of contributions
- to science. Celera Assembler is written mostly in C for unix
- operating systems. Although it requires large compute resources to
- resolve complex genomes, it can assemble bacterial genomes on a
- laptop.
- .
- This important software is an "open source" project. Originally
- developed at Celera Genomics, it was released under the GNU Public
- License and deposited on a public repository (Source Forge) in
- 2004. Scientists around the world can download, build, and run the
- software without restriction. In addition, they can inspect the
- source code and alter it at their own sites. Workers at JCVI and a
- few other institutes regularly submit their code alterations to the
- public repository.
- .
- JCVI has made many important contributions to Celera
- Assembler. Scientists and engineers at JCVI are extending the code to
- handle more and more polymorphic data sets, including environmental
- samples. In collaboration with scientists at the University of
- Maryland, they are adding the capability to assemble pyrosequencing
- data (as from a 454 FLX machine) in addition to the traditional
- Sanger sequencing data (as from an ABI 3730 machine). JCVI's efforts
- provide the cutting edge software that genome scientists around the
- world will need as they apply DNA sequencing technology to more and
- more difficult problems of biology.
- .
- See also: http://www.jcvi.org/cms/research/software/celera-assembler/overview/
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
-Depends: gbioseq
-Homepage: http://www.bioinformatics.org/project/?group_id=94
-License: GPL
-Pkg-Description: DNA sequence editor for Linux
- gBioSeq is in an early stage of development, but it is already running.
- The goal is to provide an easy to use software to edit DNA sequences under
- Linux, Windows, MacOsX, using GTK C# (Mono).
-
-Depends: phpphylotree
-Homepage: http://www.bioinformatics.org/project/?group_id=372
-License: GPL
-Pkg-Description: draw phylogenetic trees
- PhpPhylotree is a web application that is able to draw phylogenetic trees.
- It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
-
-Depends: tracetuner
-Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview
-License: GPL; but US Patent #6,681,186
-Pkg-Description: DNA sequencing and trace processing
- TraceTuner is a DNA sequencing quality value, base calling and trace
- processing software application originally developed by Paracel,
- Inc. While providing a flexible interface and capability to adopt the
- "pure" base calls produced by Phred, KB or any other "original"
- caller, it offers competitive features not currently available in
- other tools, such as customized calibration of quality values,
- advanced heterozygote and mixed base calling and deconvolving the
- "mixed" electropherograms resulting from the presence of indels into
- a couple of "pure" electropherograms. Previous versions of TraceTuner
- were used by Celera Genomics to process over 27 million reads from
- both Drosophila and human genome projects and by Applied Biosystems,
- as a component of its SNP detection and genotyping software product
- SeqScape. TraceTuner implements an advanced peak processing
- technology for resolving overlapping peaks of the same dye color into
- individual, or "intrinsic" peaks. This technology was protected by US
- Patent #6,681,186. Currently, TraceTuner is an open source software,
- which has been used by J. Craig Venter Institute's DNA Sequencing and
- Resequencing pipelines.
- .
- The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All
- rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is
- being made available free of charge by Applera Corporation subject to the terms
- and conditions of the GNU General Public License, version 2, as published by the
- Free Software Foundation (the "GNU General Public License").
-
-Depends: twain
-Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
-License: Open Source
-Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
- TWAIN is a new syntenic genefinder which employs a Generalized Pair
- Hidden Markov Model (GPHMM) to predict genes in two closely related
- eukaryotic genomes simultaneously. It utilizes the MUMmer package to
- perform approximate alignment before applying a GPHMM based on an
- enhanced version of the TigrScan gene finder. TWAIN was written by
- Bill Majoros and Mihaela Pertea while at The Institute for Genomic
- Research (TIGR).
- .
- TWAIN consists of two components: (1) ROSE, the Region Of Synteny
- Extractor, which identifies contiguous regions likely to contain one
- or more syntenic genes, and (2) OASIS, a generalized pair hidden
- Markov model (GPHMM) for predicting genes in the regions identified
- by ROSE. The system utilizes approximate alignments constructed by
- the PROmer and NUCmer programs in the MUMmer package to assess
- approximate alignment scores efficiently. More detailed information
- on the architecture of this system will be made available soon.
- Slides from a talk at Computational Genomics 2004 are now available.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Depends: rose
-Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
-License: Open Source
-Pkg-Description: Region-Of-Synteny Extractor
- ROSE is a program which identifies regions between two genomes which
- are likely to contain orthologous genes. The two genomes are given as
- two multi fasta files of DNA sequences. The PROmer program from the
- MUMmer package needs to be run first between the two genomes, and the
- resulting delta file is then input to ROSE. If a previous annotation
- is available for one or both genomes, then the coordinates of the
- annotated genes from a genome can be optionally given as input in a
- gff file. The gene coordinates will be used to guide the length of
- the regions produced by ROSE. By default, when finding a region of
- consistent alignments, ROSE will add a user-defined margin (1000 bp
- by default) on either side of that region. When a predicted gene
- overlaps an alignment we use the gene prediction to extend the
- boundaries of the output region.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Depends: glimmerhmm
-Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
-License: Artistic
-Pkg-Description: Eukaryotic Gene-Finding System
- GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
- Model (GHMM). Although the gene finder conforms to the overall
- mathematical framework of a GHMM, additionally it incorporates splice
- site models adapted from the GeneSplicer program and a decision tree
- adapted from GlimmerM. It also utilizes Interpolated Markov Models
- for the coding and noncoding models . Currently, GlimmerHMM's GHMM
- structure includes introns of each phase, intergenic regions, and
- four types of exons (initial, internal, final, and single). A basic
- user manual can be consulted here.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Depends: genezilla
-Homepage: http://www.genezilla.org/
-License: Artistic
-Language: C++
-X-Importance: state-of-art
-X-Category: Gene prediction (through GHMM)
-Pkg-Description: eukaryotic gene finder
- GeneZilla is a state-of-the-art program for computational prediction
- of protein-coding genes in eukaryotic DNA, and is based on the
- Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
- and GENIE. It is highly reconfigurable and includes software for
- retraining by the end-user. It is written in highly optimized C++ and
- runs under most UNIX/Linux platforms. The run time and memory
- requirements are linear in the sequence length, and are in general
- much better than those of competing systems, due to GeneZilla's novel
- decoding algorithm. Graph-theoretic representations of the high
- scoring open reading frames are provided, allowing for exploration of
- sub-optimal gene models. It utilizes Interpolated Markov Models
- (IMMs), Maximal Dependence Decomposition (MDD), and includes states
- for signal peptides, branch points, TATA boxes, CAP sites, and will
- soon model CpG islands as well.
- .
- GeneZilla is an open-source project hosted at bioinformatics.org and
- currently consists of ~20,000 lines of code. GeneZilla evolved out
- of the ab initio eukaryotic gene finder TIGRscan, which was developed
- at The Institute for Genomic Research over a 3-year period under NIH
- grants R01-LM06845 and R01-LM007938, and which served as the basis
- for the comparative gene finder TWAIN.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Depends: exalt
-Homepage: http://www.cbcb.umd.edu/software/exalt/
-License: Artistic
-Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
- ExAlt is a software program designed to predict alternatively spliced
- overlapping exons in genomic sequence. The program works in several
- ways depending on the available input. ExAlt can use information of
- existing gene structure as well as sequence conservation to improve
- the precision of it's predictions. ExAlt can also make predictions
- when only a single genomic sequence is available. ExAlt has been
- extensively tested on Drosophila melanogaster, but can be adapted to
- run on other species.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Depends: jigsaw
-Homepage: http://www.cbcb.umd.edu/software/jigsaw/
-License: Artistic
-Pkg-Description: gene prediction using multiple sources of evidence
- JIGSAW is a program designed to use the output from gene finders,
- splice site prediction programs and sequence alignments to predict
- gene models. The program provides an automated way to take advantage
- of the many succsessful methods for computational gene prediction and
- can provide substantial improvements in accuracy over an individual
- gene prediction program.
- .
- JIGSAW is available for all species. It is tested on Human, Rice
- (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
- neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
- fumigatus, Plasmodium falciparum and Plasmodium yoelii.
- .
- The linear combiner option is now available in the current JIGSAW
- software distribution. This allows JIGSAW to be run without the use
- of training data. A weight is assigned to each evidence source, and
- gene predictions are based on a weighted voting scheme, yielding the
- best 'consensus' predictions.
- .
- Predictions are now available for the ENCODE regions in Human and
- viewable as custom tracks in the UCSC Human Genome
- Browser. Predictions available for the Human genome and viewable as
- custom tracks in the UCSC Human Genome Browser
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Depends: genesplicer
-Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
-License: Artistic
-Pkg-Description: computational method for splice site prediction
- A fast, flexible system for detecting splice sites in the genomic DNA
- of various eukaryotes. The system has been trained and tested
- successfully on Plasmodium falciparum (malaria), Arabidopsis
- thaliana, human, Drosophila, and rice . Training data sets for human
- and Arabidopsis thaliana are included. Use the GeneSplicer Web
- Interface to run GeneSplicer directly, or see below for instructions
- on downloading the complete system including source code.
- .
- There is no independent program to train GeneSplicer, but there is a
- way to obtain the necessary files by using the training procedure of
- GlimmerHMM.
-Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
-
-Ignore: riso
-Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
-License: not specified
-Pkg-Description: motif discovery tool
- RISO discovers motifs composed of many binding sites separated by
- spacers. Each binding site is called a box
- .
- The author of SMILE claims at his homepage
- http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is
- faster and more powerfull than SMILE which is described itself as
- "SMILE is a tool that infers motifs in a set of sequences, according
- to some criterias. It was first made to infer exceptionnal sites as
- binding sites in DNA sequences. It allows to infer motifs written on
- any alphabet (even degenerate) in any kind of sequences. The
- specificity of SMILE is to allow to deal with what we call
- "structured motifs", which are motifs associated by some distance
- constraints. In particular, SMILE is able to group under a unique
- model different occurrences composed of several boxes separated by
- spacers of different lengths."
- .
- The reference to SMILE is made here especially because there is some
- work done in the Debian Med SVN at
- http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/
- .
- On the other hand the SMILE author told us in private mail that he
- thinks that RISO is dead and SMILE continues to have some importance.
-
-Depends: mummergpu
-Homepage: http://mummergpu.sourceforge.net/
-License: Artistic
-Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
- The recent availability of new, less expensive high-throughput DNA
- sequencing technologies has yielded a dramatic increase in the volume
- of sequence data that must be analyzed. These data are being
- generated for several purposes, including genotyping, genome
- resequencing, metagenomics, and de novo genome assembly
- projects. Sequence alignment programs such as MUMmer have proven
- essential for analysis of these data, but researchers will need ever
- faster, high-throughput alignment tools running on inexpensive
- hardware to keep up with new sequence technologies.
- .
- MUMmerGPU is a low cost, ultra-fast sequence alignment program
- designed to handle the increasing volume of data produced by new,
- high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in
- replacement for MUMmer, using the GPUs in common workstations to
- simultaneously align multiple query sequences against a single
- reference sequence stored as a suffix tree. By processing the queries
- in parallel on the highly parallel graphics card, MUMmerGPU achieves
- more than a 10-fold speedup over a serial CPU version of the sequence
- alignment kernel, and outperforms MUMmer on a high end CPU by
- 3.5-fold in total application time when aligning reads from recent
- sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
- technologies.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
-Depends: amos-assembler
-Homepage: http://amos.sourceforge.net/
-License: Artistic
-Language: Perl
-X-Category: Genome assembling
-Pkg-Description: modular whole genome assembler
- The AMOS consortium is committed to the development of open-source
- whole genome assembly software. The project acronym (AMOS) represents
- our primary goal -- to produce A Modular, Open-Source whole genome
- assembler. Open-source so that everyone is welcome to contribute and
- help build outstanding assembly tools, and modular in nature so that
- new contributions can be easily inserted into an existing assembly
- pipeline. This modular design will foster the development of new
- assembly algorithms and allow the AMOS project to continually grow
- and improve in hopes of eventually becoming a widely accepted and
- deployed assembly infrastructure. In this sense, AMOS is both a
- design philosophy and a software system.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
-Depends: amoscmp
-Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
-License: Artistic
-Pkg-Description: comparative genome assembly package
- A comparative assembler is a program that can assemble a set of
- shotgun reads from an organism by mapping them to the finished
- sequence of a related organism. Thus, a comparative assembler
- transforms the traditional overlap-layout-consensus approach to
- alignment-layout-consensus. The AMOScmp package uses the MUMmer
- program to perform a mapping of the reads to the reference genome,
- then processes the alignment results with a sophisticated layout
- program designed to take into account polymorphisms between the two
- genomes. For a detailed description of the algorithms involved please
- refer to the paper listed in the References section.
- .
- AMOScmp uses as AMOS messages as both the inputs and the outputs (see
- documentation). Two utilities are provided to process these files:
- tarchive2amos - a versatile converter from trace archive .seq, .qual,
- and .xml information into AMOS formatted data; amos2ace - a converter
- from AMOS formatted data to the .ACE assembly format. In addition,
- the AMOS::AmosLib Perl module is provided as a tool for users who
- prefer to write their own conversion utilities. Please see the
- documentation included with the distribution for more information.
- .
- AMOScmp is part of the AMOS package (see
- http://amos.sourceforge.net/)- a collaborative effort to develop a
- modular open-source framework for assembly development.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
-Depends: minimus
-Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
-License: Artistic
-Pkg-Description: AMOS lightweight assembler
- minimus is an assembly pipeline designed specifically for small
- data-sets, such as the set of reads covering a specific gene. Note
- that the code will work for larger assemblies (we have used it to
- assemble bacterial genomes), however, due to its stringency, the
- resulting assembly will be highly fragmented. For large and/or
- complex assemblies the execution of Minimus should be followed by
- additional processing steps, such as scaffolding.
- .
- minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
- * overlapper - computes the overlaps between the reads using a
- modified version of the Smith-Waterman local alignment algorithm
- * tigger - uses the read overlaps to generate the layouts of reads
- representing individual contigs
- * make-consensus - refines the layouts produced by the tigger to
- generate accurate multiple alignments within the reads
- .
- minimus uses as AMOS messages as both the inputs and the outputs (see
- documentation). Two utilities are provided to process these files:
- tarchive2amos - a versatile converter from trace archive .seq, .qual,
- and .xml information into AMOS formatted data; amos2ace - a converter
- from AMOS formatted data to the .ACE assembly format. In addition,
- the AMOS::AmosLib Perl module is provided as a tool for users who
- prefer to write their own conversion utilities. Please see the
- documentation included with the distribution for more information.
- .
- minimus is part of the AMOS package - a collaborative effort to
- develop a modular open-source framework for assembly development.
-Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
-
-Ignore: catissuecore
-Homepage: https://cabig.nci.nih.gov/tools/catissuecore
-License: to be clarified, NCICB Open Source Project Site
-Pkg-Description: biospecimen inventory, tracking, and basic annotation
- caTissue Core is caBIG's tissue bank repository tool for biospecimen
- inventory, tracking, and basic annotation. Version 1.2.1 of caTissue
- permits users to track the collection, storage, quality assurance,
- and distribution of specimens as well as the derivation and
- aliquotting of new specimens from an existing ones (e.g. for DNA
- analysis). It also allows users to find and request specimens that
- may then be used in molecular, correlative studies.
- .
- Intended Audiences: Translational Researchers, Pathologists, Biobank
- Managers
-Note: A lot of stuff can be found at National Cancer Institute's
- Center for Bioinformatics (NCICB) Open Source Project Site
- http://gforge.nci.nih.gov/ which has to be evaluated and put into the
- right category of our tasks files
-
-Ignore: trapss
-Homepage: https://putt.eng.uiowa.edu/
-License: Creative Commons for Science license
-Pkg-Description: Transcript Annotation Prioritization and Screening System
- TrAPSS stands for Transcript Annotation Prioritization and Screening
- System. It is a system comprised of several tools written by
- researchers at the Coordinated Lab for Computational Genomics in the
- University of Iowa. The system aims to aid scientists who are
- searching for the genetic mutation or mutations that are linked to
- expression of a disease phentotype. The system offers support for
- almost all areas of a mutation discovery project from the creation
- and prioritization of a large candidate gene list, to the selection,
- ordering, and managing of primer pairs, and even support for SSCP
- assay results. TrAPSS is a currently deployed and often used tool for
- several laboratories here at the University of Iowa in the College of
- Medicine. The system is composed of several Java applications, many
- web-based PHP tools, and a local MySQL database. Even the Java
- applications are available through a web browser due to Sun's Java
- Web Start. Director of the CLCG, Professor Terry A. Braun, heads the
- project along with Dr. Todd Scheetz and Prof. Thomas
- L. Casavant. Eight developers create and maintain the software:
- Bartley Brown , Hakeem Almabrazi, Steven Davis and Jason Grundstad;
- along with three graduate students, Brian O'Leary, John Ritchison and
- Michael Smith; and one undergraduate student, Matthew Kemp.
- Importance of TrAPSS
- .
- The true importance of TrAPSS is that it is based upon a novel way to
- examine a large candidate list of genes. Rather than sequentially
- examining full genes, the scheme often followed in current target
- identification projects, TrAPSS provides tools that offer the user
- the opportunity to screen certain small parts of several genes from
- the candidate list at once. This "parallel" screening idea was
- envisioned by researchers here at the University of Iowa including
- Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate
- students Steven Davis and Brian O'Leary has demonstrated the
- advantage of the parallel screening method over the sequential
- sequencing of large candidate lists.
-Note: Found at
- http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
-
-Depends: mage2tab
-Homepage: https://www.cbil.upenn.edu/magewiki/index.php/mage2tab
-License: CBIL Software and Data License (Apache-like)
-WNPP: 476209
-Responsible: Charles Plessy <plessy at debian.org>
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mage2tab/trunk/
-Pkg-Description: MAGE-MLv1 converter and visualiser
- This tool-kit is part of MR_T, a framework for import or export various of
- MAGE (MicroArray Gene Expression) documents (MAGE-MLv1, MAGE-TAB, SOFT,
- MINiML) from or into databases like GUS (the Genomics Unified Schema,
- www.gusdb.org).
Depends: bambus
Homepage: http://amos.sourceforge.net/docs/bambus/
More information about the Blends-commit
mailing list