[Collab-qa-commits] r2170 - in packages-metadata: a b c d e g h i k l m n p q r s t v
Charles Plessy
plessy at alioth.debian.org
Tue Mar 6 14:42:56 UTC 2012
Author: plessy
Date: 2012-03-06 14:42:56 +0000 (Tue, 06 Mar 2012)
New Revision: 2170
Added:
packages-metadata/a/adun.app.upstream
packages-metadata/a/alien-hunter.upstream
packages-metadata/a/autodock-vina.upstream
packages-metadata/a/autodock.upstream
packages-metadata/a/autodocktools.upstream
packages-metadata/a/autogrid.upstream
packages-metadata/b/ballview.upstream
packages-metadata/b/beeswarm.upstream
packages-metadata/b/biomaj.upstream
packages-metadata/b/bioperl.upstream
packages-metadata/b/bwa.upstream
packages-metadata/b/bzr-svn.upstream
packages-metadata/c/cd-hit.upstream
packages-metadata/c/circos.upstream
packages-metadata/c/clustalo.upstream
packages-metadata/c/clustalw-mpi.upstream
packages-metadata/c/clustalw.upstream
packages-metadata/c/clustalx.upstream
packages-metadata/c/cufflinks.upstream
packages-metadata/d/dialign-tx.upstream
packages-metadata/d/dialign.upstream
packages-metadata/d/dicomscope.upstream
packages-metadata/d/disulfinder.upstream
packages-metadata/e/elastix.upstream
packages-metadata/e/emboss.upstream
packages-metadata/e/epigrass.upstream
packages-metadata/e/exonerate.upstream
packages-metadata/g/glam2.upstream
packages-metadata/h/hhsuite.upstream
packages-metadata/h/hmmer.upstream
packages-metadata/i/infernal.upstream
packages-metadata/k/kalign.upstream
packages-metadata/l/last-align.upstream
packages-metadata/l/libbio-graphics-perl.upstream
packages-metadata/l/libtfbs-perl.upstream
packages-metadata/m/mafft.upstream
packages-metadata/m/maq.upstream
packages-metadata/m/maude.upstream
packages-metadata/m/melting-gui.upstream
packages-metadata/m/melting.upstream
packages-metadata/m/mipe.upstream
packages-metadata/m/mira-assembler.upstream
packages-metadata/m/mothur.upstream
packages-metadata/m/mummer.upstream
packages-metadata/m/mustang.upstream
packages-metadata/n/ncoils.upstream
packages-metadata/p/perlprimer.upstream
packages-metadata/p/phyml.upstream
packages-metadata/p/poa.upstream
packages-metadata/p/primer3.upstream
packages-metadata/p/probalign.upstream
packages-metadata/p/probcons.upstream
packages-metadata/p/proda.upstream
packages-metadata/q/qiime.upstream
packages-metadata/r/r-bioc-limma.upstream
packages-metadata/r/r-cran-epitools.upstream
packages-metadata/r/r-cran-haplo.stats.upstream
packages-metadata/r/r-cran-qtl.upstream
packages-metadata/r/r-cran-qvalue.upstream
packages-metadata/r/r-cran-randomforest.upstream
packages-metadata/r/r-cran-rocr.upstream
packages-metadata/r/r-other-bio3d.upstream
packages-metadata/r/r-other-mott-happy.upstream
packages-metadata/r/raster3d.upstream
packages-metadata/r/raxml.upstream
packages-metadata/r/rnahybrid.upstream
packages-metadata/s/samtools.upstream
packages-metadata/s/seaview.upstream
packages-metadata/s/seqan-apps.upstream
packages-metadata/s/seqan-dev.upstream
packages-metadata/s/sigma-align.upstream
packages-metadata/s/ssake.upstream
packages-metadata/t/t-coffee.upstream
packages-metadata/t/tm-align.upstream
packages-metadata/t/tophat.upstream
packages-metadata/t/transtermhp.upstream
packages-metadata/t/treeviewx.upstream
packages-metadata/v/velvet.upstream
Log:
Collected 78 debian/upstream files.
Added: packages-metadata/a/adun.app.upstream
===================================================================
--- packages-metadata/a/adun.app.upstream (rev 0)
+++ packages-metadata/a/adun.app.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,24 @@
+Archive: Gna
+Reference-DOI: 10.1002/jcc.20312
+Homepage: http://diana.imim.es/Adun
+Name: Adun
+Reference-PMID: 16175583
+Reference:
+ Author: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa
+ Title: >
+ Framework-based design of a new all-purpose molecular simulation application: The Adun simulator
+ Journal: J. Comp. Chem.
+ Volume: 26
+ Number: 15
+ Pages: 1647-1659
+ Year: 2005
+ URL: http://www3.interscience.wiley.com/journal/112094040/abstract
+Screenshots: http://cbbl.imim.es:8080/Adun/screenshots
+Watch: |
+ version=3
+ # Upstream used a broken versioning scheme where a major release is
+ # 0.7 and point releases are 0.71, 0.72, etc. Hopefully this is no
+ # longer a concern, but if it turns out it is, uncommenting and
+ # amending the line below should "fix" the watchfile accordingly.
+ #opts=uversionmangle=s/^0\.([78])(\d)/0.$1.$2/, \
+ http://download.gna.org/adun/Adun-([\d.]+)\.tar\.gz
Added: packages-metadata/a/alien-hunter.upstream
===================================================================
--- packages-metadata/a/alien-hunter.upstream (rev 0)
+++ packages-metadata/a/alien-hunter.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,18 @@
+Contact : George Vernikos <gsv at sanger.ac.uk>
+Reference-DOI: 10.1093/bioinformatics/btl369
+Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html
+Name: Alien_hunter
+Reference-PMID: 16837528
+Reference:
+ author: Vernikos, Georgios S. and Parkhill, Julian
+ title: >
+ Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
+ journal: Bioinformatics
+ volume: 22
+ number: 18
+ pages: 2196-2203
+ doi: 10.1093/bioinformatics/btl369
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2196
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/18/2196.pdf
+Watch: http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz
Added: packages-metadata/a/autodock-vina.upstream
===================================================================
--- packages-metadata/a/autodock-vina.upstream (rev 0)
+++ packages-metadata/a/autodock-vina.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Contact: Oleg Trott <ot14 at columbia.edu>
+Reference-DOI: 10.1002/jcc.21334
+Homepage: http://vina.scripps.edu
+Name: AutoDock Vina
+Reference:
+ author: Oleg Trott, Arthur J. Olson
+ title: >
+ AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
+ journal: Journal of Computational Chemistry
+ volume: 31
+ number: 2
+ pages: 455-461
+ year: 2010
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21334/full
Added: packages-metadata/a/autodock.upstream
===================================================================
--- packages-metadata/a/autodock.upstream (rev 0)
+++ packages-metadata/a/autodock.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+Reference-DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDock
+Reference-PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
+ Title: >
+ AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+ Journal: Journal of Computational Chemistry
+ Volume: 30
+ Number: 16
+ Pages: 2785-2791
+ Year: 2009
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: |
+ opts="dversionmangle=s/\+rc/~rc/" \
+ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
Added: packages-metadata/a/autodocktools.upstream
===================================================================
--- packages-metadata/a/autodocktools.upstream (rev 0)
+++ packages-metadata/a/autodocktools.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,26 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+Reference-DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDockTools
+Reference-PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
+ Title: >
+ AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+ Journal: Journal of Computational Chemistry
+ Volume: 30
+ Number: 16
+ Pages: 2785-2791
+ Year: 2009
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Reference:
+ Author: Harris R, Olson AJ, Goodsell DS.
+ Title: >
+ Automated prediction of ligand-binding sites in proteins.
+ Journal: Proteins
+ Year: 2008
+ Volume: 70
+ Number: 4
+ Pages: 1506-1517
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz
Added: packages-metadata/a/autogrid.upstream
===================================================================
--- packages-metadata/a/autogrid.upstream (rev 0)
+++ packages-metadata/a/autogrid.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
+Reference-DOI: 10.1002/jcc.21256
+Homepage: http://autodock.scripps.edu/
+Name: AutoDock
+Reference-PMID: 19399780
+Reference:
+ Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson.
+ Title: >
+ AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
+ Journal: Journal of Computational Chemistry
+ Volume: 30
+ Number: 16
+ Pages: 2785-2791
+ Year: 2009
+ URL: http://www3.interscience.wiley.com/journal/122365050/abstract
+Registration: http://autodock.scripps.edu/downloads/autodock-registration
+Watch: |
+ opts="dversionmangle=s/\+rc/~rc/" \
+ http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ \.\./autodock-registration/tars/.*/autodocksuite-(.*)-src\.tar\.gz
Added: packages-metadata/b/ballview.upstream
===================================================================
--- packages-metadata/b/ballview.upstream (rev 0)
+++ packages-metadata/b/ballview.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,21 @@
+# Collection of meta-data about the upstream project,
+# see http://wiki.debian.org/UpstreamMetadata for reference.
+Contact: BALL authors <ball at bioinf.uni-sb.de>
+Homepage: http://www.ballview.org
+Name: BALL
+Reference:
+ author: Moll, Andreas and Hildebrandt, Andreas and Lenhof, Hans-Peter and Kohlbacher, Oliver
+ title: >
+ BALLView: a tool for research and education in molecular modeling
+ journal: Bioinformatics
+ volume: 22
+ number: 3
+ pages: 365-366
+ year: 2006
+ PMID: 16332707
+ DOI: 10.1093/bioinformatics/bti818
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/3/365
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/3/365.pdf
+Watch: |
+ opts=uversionmangle=s/-(.*)/+$1/ \
+ http://ball-www.bioinf.uni-sb.de/Releases/all/BALL-(.*)\.tar\.gz
Added: packages-metadata/b/beeswarm.upstream
===================================================================
--- packages-metadata/b/beeswarm.upstream (rev 0)
+++ packages-metadata/b/beeswarm.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,4 @@
+Contact: Aron Charles Eklund <eklund+beeswarm at cbs.dtu.dk>
+CRAN: http://cran.r-project.org/web/packages/beeswarm
+Homepage: http://www.cbs.dtu.dk/~eklund/beeswarm/
+Name: beeswarm
Added: packages-metadata/b/biomaj.upstream
===================================================================
--- packages-metadata/b/biomaj.upstream (rev 0)
+++ packages-metadata/b/biomaj.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,11 @@
+Reference-DOI: 10.1093/bioinformatics/btn325
+Homepage: http://biomaj.genouest.org
+Reference:
+ Author: Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy and David Allouche
+ Title: >
+ BioMAJ: a flexible framework for databanks synchronization and processing
+ Journal: Oxford Journals Bioinformatics
+ Year: 2008
+ URL: http://bioinformatics.oxfordjournals.org/content/24/16/1823.abstract
+Repository: https://gforge.inria.fr/scm/?group_id=369
+Screenshots: http://biomaj.genouest.org/?page_id=449
Added: packages-metadata/b/bioperl.upstream
===================================================================
--- packages-metadata/b/bioperl.upstream (rev 0)
+++ packages-metadata/b/bioperl.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,20 @@
+Bug-Database: https://redmine.open-bio.org/projects/bioperl
+Contact: Bioperl developers <bioperl-l at bioperl.org>
+Reference-DOI: 10.1101/gr.361602
+Homepage: http://www.bioperl.org/
+Name: BioPerl
+Reference-PMID: 12368254
+Reference:
+ author: >
+ J.E. Stajich and D. Block and K. Boulez and S.E. Brenner
+ and S.A. Chervitz and C. Dagdigian and G. Fuellen and J.G. Gilbert
+ and I. Korf and H. Lapp and H. Lehvaslaiho and C. Matsalla and
+ C.J. Mungall and B.I. Osborne and M.R. Pocock and P. Schattner and
+ M. Senger and L.D. Stein and E. Stupka and M.D. Wilkinson and E. Birney
+ title: "The Bioperl toolkit: Perl modules for the life sciences."
+ journal: Genome Res.
+ year: 2002
+ volume: 12
+ number: 10
+ pages: 1611-1618
+Repository: https://github.com/bioperl/bioperl-live
Added: packages-metadata/b/bwa.upstream
===================================================================
--- packages-metadata/b/bwa.upstream (rev 0)
+++ packages-metadata/b/bwa.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,20 @@
+Archive: SourceForge
+FAQ: http://bio-bwa.sourceforge.net/
+Homepage: http://bio-bwa.sourceforge.net/
+Name: Burrows-Wheeler Aligner
+Reference:
+ Article: HengLi07152009
+ Author: Li, Heng and Durbin, Richard
+ Title: Fast and accurate short read alignment with Burrows-Wheeler transform
+ Journal: Bioinformatics
+ Volume: 25
+ Number: 14
+ Pages: 1754-1760
+ Year: 2009
+ DOI: 10.1093/bioinformatics/btp324
+ PMID: 19451168
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754
+ Eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/14/1754.pdf
+References: http://bio-bwa.sourceforge.net/
+Repository: https://github.com/lh3/bwa.git
+Repository-Browse: https://github.com/lh3/bwa
Added: packages-metadata/b/bzr-svn.upstream
===================================================================
Added: packages-metadata/c/cd-hit.upstream
===================================================================
--- packages-metadata/c/cd-hit.upstream (rev 0)
+++ packages-metadata/c/cd-hit.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,13 @@
+Contact: Weizhong Li <liwz at sdsc.edu>
+Reference-DOI: 10.1093/bioinformatics/btl158
+Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
+Name: CD-HIT
+Reference-PMID: 16731699
+Reference:
+ author: Weizhong Li, Adam Godzik
+ title: >
+ Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
+ journal: Bioinformatics
+ volume: 22
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/content/22/13/1658.full.pdf+html
Added: packages-metadata/c/circos.upstream
===================================================================
--- packages-metadata/c/circos.upstream (rev 0)
+++ packages-metadata/c/circos.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,11 @@
+Reference-DOI: 10.1101/gr.092759.109
+Homepage: http://circos.ca/
+Reference:
+ Author: Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, and Marco A Marra
+ Title: >
+ Circos: An information aesthetic for comparative genomics
+ Journal: Genome Research
+ Year: 2009
+ URL: http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.full.pdf+html
+Repository: http://circos.ca/software/download/
+Screenshots: http://circos.ca/tutorials/images/small/
Added: packages-metadata/c/clustalo.upstream
===================================================================
--- packages-metadata/c/clustalo.upstream (rev 0)
+++ packages-metadata/c/clustalo.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,13 @@
+Contact: Fabian Sievers (UCD Dublin, Ireland)
+Reference-DOI: 10.1038/msb.2011.75
+Homepage: http://www.clustal.org/omega/
+Name: Clustal Omega
+Reference-PMID: 21988835
+Reference:
+ author: Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson and Desmond G Higgins
+ title: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
+ journal: Molecular Systems Biology
+ volume: 7
+ number: 539
+ year: 2011
+ URL: http://www.nature.com/msb/journal/v7/n1/full/msb201175.html
Added: packages-metadata/c/clustalw-mpi.upstream
===================================================================
--- packages-metadata/c/clustalw-mpi.upstream (rev 0)
+++ packages-metadata/c/clustalw-mpi.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,14 @@
+Contact: Dr. Kuo-Bin Li <kbli at ym.edu.tw>
+Name: ClustalW-MPI
+Homepage: http://www.bii.a-star.edu.sg/achievements/applications/clustalw/
+Remark: The source is only available in a previous version (0.13) at the homepage
+Reference:
+ author: Kuo-Bin Li
+ title: "ClustalW-MPI: ClustalW Analysis Using Distributed and Parallel Computing"
+ journal: Bioinformatics
+ volume: 19
+ number: 12
+ pages: 1585-1586
+ year: 2003
+ DOI: 10.1093/bioinformatics/btg192
+ PMID: 12912844
Added: packages-metadata/c/clustalw.upstream
===================================================================
--- packages-metadata/c/clustalw.upstream (rev 0)
+++ packages-metadata/c/clustalw.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,18 @@
+Bugs: http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal
+Contact: clustalw at ucd.ie
+Homepage: http://www.clustal.org/
+Reference:
+ author: Larkin, M.A. and Blackshields, G. and Brown, N.P. and Chenna, R. and McGettigan, P.A. and McWilliam, H. and Valentin, F. and Wallace, I.M. and Wilm, A. and Lopez, R. and Thompson, J.D. and Gibson, T.J. and Higgins, D.G.
+ title: Clustal W and Clustal X version 2.0
+ journal: Bioinformatics
+ volume: 23
+ number: 21
+ pages: 2947-2948
+ year: 2007
+ PMID: 17846036
+ DOI: 10.1093/bioinformatics/btm404
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2947
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2947.pdf
+Webservice:
+ - http://www.ebi.ac.uk/Tools/clustalw2/
+ - http://www.ch.embnet.org/software/ClustalW.html
Added: packages-metadata/c/clustalx.upstream
===================================================================
--- packages-metadata/c/clustalx.upstream (rev 0)
+++ packages-metadata/c/clustalx.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Bugs: http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal
+Contact: clustalw at ucd.ie
+Homepage: http://www.clustal.org/
+Reference:
+ author: Larkin, M.A. and Blackshields, G. and Brown, N.P. and Chenna, R. and McGettigan, P.A. and McWilliam, H. and Valentin, F. and Wallace, I.M. and Wilm, A. and Lopez, R. and Thompson, J.D. and Gibson, T.J. and Higgins, D.G.
+ title: Clustal W and Clustal X version 2.0
+ journal: Bioinformatics
+ volume: 23
+ number: 21
+ pages: 2947-2948
+ year: 2007
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2947
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2947.pdf
+ DOI: 10.1093/bioinformatics/btm404
+ PMID: 17846036
Added: packages-metadata/c/cufflinks.upstream
===================================================================
--- packages-metadata/c/cufflinks.upstream (rev 0)
+++ packages-metadata/c/cufflinks.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,10 @@
+Contact: Cole Trapnell <cole at cs.umd.edu>
+Homepage: http://cufflinks.cbcb.umd.edu/
+Name: Cufflinks
+Reference:
+ Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
+ Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
+ Journal: Nature Biotechnology
+ DOI: doi:10.1038/nbt.1621
+ URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
+ Year: 2010
Added: packages-metadata/d/dialign-tx.upstream
===================================================================
--- packages-metadata/d/dialign-tx.upstream (rev 0)
+++ packages-metadata/d/dialign-tx.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,18 @@
+Contact: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+Reference-DOI: 10.1186/1748-7188-3-6
+Homepage: http://dialign-tx.gobics.de/
+Reference-PMID: 18505568
+Name: DIALIGN-T
+Reference:
+ AUTHOR: Subramanian, Amarendran and Kaufmann, Michael and Morgenstern, Burkhard
+ TITLE: >
+ DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
+ JOURNAL: Algorithms for Molecular Biology
+ VOLUME: 3
+ YEAR: 2008
+ NUMBER: 1
+ PAGES: 6
+ URL: http://www.almob.org/content/3/1/6
+ DOI: 10.1186/1748-7188-3-6
+ ISSN: 1748-7188
+Watch: http://dialign-tx.gobics.de/download http://dialign-tx.gobics.de/DIALIGN-TX_(.*)\.tar\.gz
Added: packages-metadata/d/dialign.upstream
===================================================================
--- packages-metadata/d/dialign.upstream (rev 0)
+++ packages-metadata/d/dialign.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Reference-DOI: 10.1093/bioinformatics/15.3.211
+Name: DIALIGN
+Homepage: http://dialign.gobics.de/
+Reference-PMID: 10222408
+Reference:
+ Author: Morgenstern, B
+ Title: >
+ DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
+ Journal: Bioinformatics
+ Volume: 15
+ Number: 3
+ Pages: 211-218
+ Year: 1999
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/3/211
+ Eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/15/3/211.pdf
+Watch: http://dialign.gobics.de/download/dialign-(.*)-linux\.i586\.tar\.gz
Added: packages-metadata/d/dicomscope.upstream
===================================================================
--- packages-metadata/d/dicomscope.upstream (rev 0)
+++ packages-metadata/d/dicomscope.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,2 @@
+Donation: http://dicom.offis.de/donation.php.en
+Homepage: http://dicom.offis.de/dscope.php.en
Added: packages-metadata/d/disulfinder.upstream
===================================================================
--- packages-metadata/d/disulfinder.upstream (rev 0)
+++ packages-metadata/d/disulfinder.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,34 @@
+Name: disulfinder
+Reference:
+ - Author: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi
+ Title: 'DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.'
+ Journal: Nucleic Acids Res
+ Volume: 34
+ Number: Web Server issue
+ Pages: W177-81
+ Year: 2006
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986
+ PMID: 16844986
+ - Comment: For the disulphide connectivity predictor
+ Author: Vullo, Alessandro, and Frasconi, Paolo
+ Title: Disulfide connectivity prediction using recursive neural networks and evolutionary information.
+ Journal: Bioinformatics
+ Volume: 20
+ Number: 5
+ Pages: 653-9
+ Year: 2004
+ Month: March
+ PMID: 15033872
+ - Comment: For the cystein bonding state predictor
+ Author: A. Ceroni, P. Frasconi, A. Passerini and A. Vullo
+ Title: Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines
+ Journal: Journal of VLSI Signal Processing
+ Volume: 35
+ Pages: 287-295
+ Year: 2003
+ - Comment: For the cystein bonding state predictor
+ Author: P. Frasconi, A. Passerini and A. Vullo
+ Title: A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines
+ Journal: Proc. IEEE Workshop on Neural Networks for Signal Processing
+ Pages: 25-34
+ Year: 2002
Added: packages-metadata/e/elastix.upstream
===================================================================
--- packages-metadata/e/elastix.upstream (rev 0)
+++ packages-metadata/e/elastix.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,13 @@
+Contact: Stefan Klein and Marius Staring
+Homepage: http://elastix.isi.uu.nl/
+Name: Elastix
+Reference:
+ author: S. Klein, M. Staring, K. Murphy, M. A. Viergever, J. Pluim
+ title: >
+ elastix: A Toolbox for Intensity-Based Medical Image Registration
+ journal: IEEE Transactions on Medical Imaging
+ volume: 29
+ number: 1
+ pages: 196 - 205
+ year: 2010
+ URL: http://ieeexplore.ieee.org/xpls/abs_all.jsp?tp=&arnumber=5338015&isnumber=5371922
Added: packages-metadata/e/emboss.upstream
===================================================================
--- packages-metadata/e/emboss.upstream (rev 0)
+++ packages-metadata/e/emboss.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: EMBOSS core development team <emboss-bug at emboss.open-bio.org>
+Homepage: http://emboss.sourceforge.net
+Name: EMBOSS
+Reference-title: >
+ EMBOSS: The European Molecular Biology Open Software Suite
+Reference-journal: Trends in Genetics
+Reference-volume: 16
+Reference-number: 6
+Reference-pages: 276 - 277
+Reference-year: 2000
+Reference-issn: 0168-9525
+Reference-url: http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317
+Reference-author: Peter Rice and Ian Longden and Alan Bleasby
+Reference-PMID: 10827456
+Reference-DOI: 10.1016/S0168-9525(00)02024-2
+Watch: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-([\d.]*)\.tar\.gz
Added: packages-metadata/e/epigrass.upstream
===================================================================
--- packages-metadata/e/epigrass.upstream (rev 0)
+++ packages-metadata/e/epigrass.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Flavio Codeco Coelho <fccoelho at gmail.com>
+Homepage: http://epigrass.sourceforge.net/
+Name: EpiGrass
+Watch: http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz
+Reference:
+ author: Coelho, Flavio and Cruz, Oswaldo and Codeco, Claudia
+ DOI: 10.1186/1751-0473-3-3
+ title: "Epigrass: a tool to study disease spread in complex networks"
+ journal: Source Code for Biology and Medicine
+ volume: 3
+ year: 2008
+ number: 1
+ pages: 3
+ PMID: 18302744
+ URL: http://www.scfbm.org/content/3/1/3
+ ISSN: 1751-0473
Added: packages-metadata/e/exonerate.upstream
===================================================================
--- packages-metadata/e/exonerate.upstream (rev 0)
+++ packages-metadata/e/exonerate.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Guy St.C. Slater <guy AT ebi.ac.uk>
+Reference-DOI: 10.1186/1471-2105-6-31
+Name: Exonerate
+Homepage: http://www.ebi.ac.uk/~guy/exonerate/
+Reference-PMID: 15713233
+Reference:
+ Author: Slater, Guy and Birney, Ewan
+ Title: Automated generation of heuristics for biological sequence comparison
+ Journal: BMC Bioinformatics
+ Volume: 6
+ Year: 2005
+ Number: 1
+ Pages: 31
+ URL: http://www.biomedcentral.com/1471-2105/6/31
+ ISSN: 1471-2105
+Watch: http://www.ebi.ac.uk/~guy/exonerate/exonerate-([0-9.]*)\.tar\.gz
Added: packages-metadata/g/glam2.upstream
===================================================================
--- packages-metadata/g/glam2.upstream (rev 0)
+++ packages-metadata/g/glam2.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Martin C Frith <martin at cbrc.jp> and Timothy L Bailey <t.bailey at imb.uq.edu.au>
+Reference-DOI: 10.1371/journal.pcbi.1000071
+Homepage: http://bioinformatics.org.au/glam2/
+Name: GLAM2
+Reference-PMID: 18437229
+Reference:
+ author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.
+ journal: PLoS Comput Biol
+ publisher: Public Library of Science
+ title: Discovering Sequence Motifs with Arbitrary Insertions and Deletions
+ year: 2008
+ month: 05
+ volume: 4
+ url: http://dx.plos.org/10.1371/journal.pcbi.1000071
+ pages: e1000071
+ number: 5
+Watch: http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip
Added: packages-metadata/h/hhsuite.upstream
===================================================================
--- packages-metadata/h/hhsuite.upstream (rev 0)
+++ packages-metadata/h/hhsuite.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Name: hhsuite
+Contact: Andreas Hauser <hauser at genzentrum.lmu.de>
+Homepage: http://toolkit.genzentrum.lmu.de/hhblits
+Reference:
+ Author: Remmert M., Biegert A., Hauser A., and Soding J.
+ Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.'
+ Journal: Nat. Methods
+ DOI: 10.1038/NMETH.1818.
+ year: 2011
+ URL: http://www.ncbi.nlm.nih.gov/pubmed/22198341
+ PMID: 22198341
+# Author: Soding J.
+# Title: Protein homology detection by HMM-HMM comparison.
+# Journal: Bioinformatics
+# Volume: 21
+# Pages: 951-960
+# Year: 2005
+# URL: http://www.ncbi.nlm.nih.gov/pubmed/15531603
+# PMID: 15531603
Added: packages-metadata/h/hmmer.upstream
===================================================================
--- packages-metadata/h/hmmer.upstream (rev 0)
+++ packages-metadata/h/hmmer.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Contact: http://selab.janelia.org/people/eddys/contact.html
+Reference-DOI: 10.1093/bioinformatics/14.9.755
+Name: HMMER
+Homepage: http://hmmer.janelia.org
+Reference-PMID: 9918945
+Reference:
+ Author: Eddy, SR
+ Title: Profile hidden Markov models
+ Journal: Bioinformatics
+ Volume: 14
+ Number: 9
+ Pages: 755-763
+ Year: 1998
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
+Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Added: packages-metadata/i/infernal.upstream
===================================================================
--- packages-metadata/i/infernal.upstream (rev 0)
+++ packages-metadata/i/infernal.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,14 @@
+Reference-DOI: 10.1093/bioinformatics/btp157
+Homepage: http://infernal.janelia.org/
+Reference-PMID: 19307242
+Reference:
+ author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
+ title: "Infernal 1.0: inference of RNA alignments"
+ journal: Bioinformatics
+ volume: 25
+ number: 10
+ pages: 1335-1337
+ doi: 10.1093/bioinformatics/btp157
+ year: 2009
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/10/1335
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/25/10/1335.pdf
Added: packages-metadata/k/kalign.upstream
===================================================================
--- packages-metadata/k/kalign.upstream (rev 0)
+++ packages-metadata/k/kalign.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Contact: Timo Lassmann <timolassmann at gmail.com>
+Reference-DOI: 10.1093/nar/gkn1006
+Name: Kalign
+Homepage: http://msa.cgb.ki.se
+Reference-PMID: 19103665
+Reference:
+ Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.
+ Journal: Nucl. Acids Res.
+ Number: 3
+ Pages: 858-865
+ Title: "Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features"
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/37/3/858
+ Volume: 37
+ Year: 2009
+Watch: NA
Added: packages-metadata/l/last-align.upstream
===================================================================
--- packages-metadata/l/last-align.upstream (rev 0)
+++ packages-metadata/l/last-align.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,22 @@
+Contact: last (ATmark) cbrc (dot) jp
+Reference-DOI: 10.1093/nar/gkq010
+Name: LAST
+Homepage: http://last.cbrc.jp/
+Reference-PMID: 20110255
+Reference:
+ author: Frith, Martin C. and Wan, Raymond and Horton, Paul
+ title: Incorporating sequence quality data into alignment improves DNA read mapping
+ journal: Nucl. Acids Res.
+ volume: 38
+ number: 7
+ pages: e100
+ doi: 10.1093/nar/gkq010
+ year: 2010
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/38/7/e100
+ eprint: http://nar.oxfordjournals.org/cgi/reprint/38/7/e100.pdf
+ PMID: 20110255
+Repository:
+ Browse: http://last.cbrc.jp/last/
+ Checkout: svn co http://last.cbrc.jp/last
+Watch:
+Webservice: http://lastweb.cbrc.jp/
Added: packages-metadata/l/libbio-graphics-perl.upstream
===================================================================
--- packages-metadata/l/libbio-graphics-perl.upstream (rev 0)
+++ packages-metadata/l/libbio-graphics-perl.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,5 @@
+Archive: CPAN
+Contact: Lincoln Stein <lincoln.stein at oicr.on.ca>
+Homepage: http://search.cpan.org/dist/Bio-Graphics/
+Name: Bio::Graphics
+Watch: http://search.cpan.org/dist/Bio-Graphics/ .*/Bio-Graphics-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
Added: packages-metadata/l/libtfbs-perl.upstream
===================================================================
--- packages-metadata/l/libtfbs-perl.upstream (rev 0)
+++ packages-metadata/l/libtfbs-perl.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Boris.Lenhard at bccs.uib.no
+Reference-DOI: 10.1093/bioinformatics/18.8.1135
+Homepage: http://tfbs.genereg.net/
+Name: TFBS
+Reference-PMID: 12176838
+Reference-Journal: Bioinformatics
+Reference-Title: >
+ TFBS: Computational framework for transcription factor binding site analysis
+Reference-Authors: Lenhard, Boris and Wasserman, Wyeth W.
+Reference-Volume: 18
+Reference-Number: 8
+Reference-Pages: 1135-1136
+Reference-Year: 2002
+Reference-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/8/1135
+Repository: http://www.ii.uib.no/svn/lenhard/TFBS/
+Watch: http://tfbs.genereg.net/TFBS-(.*)\.tar\.gz
Added: packages-metadata/m/mafft.upstream
===================================================================
--- packages-metadata/m/mafft.upstream (rev 0)
+++ packages-metadata/m/mafft.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Contact: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
+Reference-DOI: 10.1093/bib/bbn013
+Name: MAFFT
+Homepage: http://mafft.cbrc.jp/alignment/software/
+Reference-PMID: 18372315
+Reference-Author: Katoh, Kazutaka and Toh, Hiroyuki
+Reference-Journal: Brief Bioinform
+Reference-Number: 4
+Reference-Pages: 286-298
+Reference-Title: Recent developments in the MAFFT multiple sequence alignment program
+Reference-URL: http://bib.oxfordjournals.org/cgi/content/abstract/9/4/286
+Reference-Volume: 9
+Reference-Year: 2008
+Watch: |
+ http://mafft.cbrc.jp/alignment/software/source.html mafft-(.*)-with-extensions-src.tgz
Added: packages-metadata/m/maq.upstream
===================================================================
--- packages-metadata/m/maq.upstream (rev 0)
+++ packages-metadata/m/maq.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,20 @@
+Archive: SourceForge
+Contact: Heng Li <lh3 at sanger.ac.uk>
+Reference-DOI: 10.1101/gr.078212.108
+FAQ: http://maq.sourceforge.net/faq.shtml
+Name: Maq
+Homepage: http://maq.sourceforge.net/
+Reference-PMID: 18714091
+Reference:
+ author: Li, Heng and Ruan, Jue and Durbin, Richard
+ title: Mapping short DNA sequencing reads and calling variants using mapping quality scores
+ journal: Genome Research
+ volume: 18
+ number: 11
+ pages: 1851-1858
+ doi: 10.1101/gr.078212.108
+ year: 2008
+ URL: http://genome.cshlp.org/content/18/11/1851.abstract
+ eprint: http://genome.cshlp.org/content/18/11/1851.full.pdf+html
+Watch: |
+ http://sf.net/maq/maq-([\d\.]+)\.tar\.bz2
Added: packages-metadata/m/maude.upstream
===================================================================
--- packages-metadata/m/maude.upstream (rev 0)
+++ packages-metadata/m/maude.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,14 @@
+Contact: Richard J. Wagner
+Reference-DOI: 10.1145/272991.272995
+Homepage: http://www-personal.umich.edu/~wagnerr/MersenneTwister.html
+Name: Mersenne Twister Random Number Generator
+Reference:
+ author: M. Matsumoto and T. Nishimura
+ title: >
+ Mersenne Twister: A 623-Dimensionally Equidistributed Uniform Pseudo-Random Number Generator
+ journal: ACM Transactions on Modeling and Computer Simulation
+ volume: 8
+ number: 1
+ year: 1998
+ pages: 3-30
+ URL: http://dl.acm.org/citation.cfm?id=272995
Added: packages-metadata/m/melting-gui.upstream
===================================================================
--- packages-metadata/m/melting-gui.upstream (rev 0)
+++ packages-metadata/m/melting-gui.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
+Reference-DOI: 10.1093/bioinformatics/17.12.1226
+Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
+Name: MELTING
+Reference-PMID: 11751232
+Reference:
+ author: Le Novère, Nicolas
+ title: MELTING, computing the melting temperature of nucleic acid duplex
+ journal: Bioinformatics
+ volume: 17
+ number: 12
+ pages: 1226-1227
+ year: 2001
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
+Screenshot: http://www.ebi.ac.uk/compneur-srv/melting/melting.jpg
+Webservice: http://www.ebi.ac.uk/compneur-srv/melting/melt.php
Added: packages-metadata/m/melting.upstream
===================================================================
--- packages-metadata/m/melting.upstream (rev 0)
+++ packages-metadata/m/melting.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
+Reference-DOI: 10.1093/bioinformatics/17.12.1226
+Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
+Name: MELTING
+Reference-PMID: 11751232
+Reference:
+ author: Le Novère, Nicolas
+ title: MELTING, computing the melting temperature of nucleic acid duplex
+ journal: Bioinformatics
+ volume: 17
+ number: 12
+ pages: 1226-1227
+ year: 2001
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
+Screenshot: http://www.ebi.ac.uk/compneur-srv/melting/melting.jpg
+Webservice: http://www.ebi.ac.uk/compneur-srv/melting/melt.php
Added: packages-metadata/m/mipe.upstream
===================================================================
--- packages-metadata/m/mipe.upstream (rev 0)
+++ packages-metadata/m/mipe.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,13 @@
+Archive: SourceForge
+Contact: Jan Aerts (aerts at users.sourceforge.net)
+Homepage: http://mipe.sourceforge.net
+Reference:
+ Author: Aerts J & Veenendaal T.
+ Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
+ Journal: Online Journal of Bioinformatics
+ Number: 2
+ Volume: 6
+ Pages: 114-120
+ Year: 2005
+ URL: http://users.comcen.com.au/~journals/mipeabs2005.htm
+Watch: http://sf.net/mipe/ mipe-(.*)\.tar.gz
Added: packages-metadata/m/mira-assembler.upstream
===================================================================
--- packages-metadata/m/mira-assembler.upstream (rev 0)
+++ packages-metadata/m/mira-assembler.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Bugs: http://sourceforge.net/apps/trac/mira-assembler/newticket
+Homepage: http://www.chevreux.org/projects_mira.html
+Homepage: http://sourceforge.net/apps/trac/mira-assembler
+Reference:
+ author: Chevreux, Bastien and Pfisterer, Thomas and Drescher, Bernd and Driesel, Albert J. and Müller, Werner E.G. and Wetter, Thomas and Suhai, Sándor
+ title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
+ journal: Genome Research
+ volume: 14
+ number: 6
+ pages: 1147-1159
+ PMID: 15140833
+ doi: 10.1101/gr.1917404
+ year: 2004
+ URL: http://genome.cshlp.org/content/14/6/1147.abstract
+ eprint: http://genome.cshlp.org/content/14/6/1147.full.pdf+htm
Added: packages-metadata/m/mothur.upstream
===================================================================
--- packages-metadata/m/mothur.upstream (rev 0)
+++ packages-metadata/m/mothur.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Patrick D. Schloss <pschloss at umich.edu>
+Reference-DOI: 10.1128/AEM.01541-09
+Homepage: http://www.mothur.org
+Reference-PMID: 19801464
+Name: Mothur
+Reference:
+ AUTHOR: Schloss, P.D., et al.
+ TITILE: >
+ Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
+ JOURNAL: Appl Environ Microbiol
+ YEAR: 2009
+ PAGES: 7537-7541
+ VOLUME: 75
+ NUMBER: 23
+ URL: http://aem.asm.org/cgi/content/full/75/23/7537
+ ISSN: 1098-5336
Added: packages-metadata/m/mummer.upstream
===================================================================
--- packages-metadata/m/mummer.upstream (rev 0)
+++ packages-metadata/m/mummer.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Archive: SourceForge
+Homepage: http://mummer.sourceforge.net/
+Reference:
+ Author: Kurtz, Stefan and Phillippy, Adam and Delcher, Arthur and Smoot, Michael and Shumway, Martin and Antonescu, Corina and Salzberg, Steven
+ Title: Versatile and open software for comparing large genomes
+ Journal: Genome Biology
+ Volume: 5
+ Year: 2004
+ Number: 2
+ Pages: R12
+ URL: http://genomebiology.com/2004/5/2/R12
+ PMID: 14759262
+ DOI: 10.1186/gb-2004-5-2-r12
+ ISSN: 1465-6906
+Repository: http://mummer.cvs.sourceforge.net/mummer/
+Screenshots: http://sourceforge.net/project/screenshots.php?group_id=133157
Added: packages-metadata/m/mustang.upstream
===================================================================
--- packages-metadata/m/mustang.upstream (rev 0)
+++ packages-metadata/m/mustang.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun)
+Reference-DOI: 10.1002/prot.20921
+Homepage: http://www.cs.mu.oz.au/~arun/mustang/
+Name: MUSTANG
+Reference-PMID: 16736488
+Reference:
+ Author: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk
+ Title: >
+ MUSTANG: A multiple structural alignment algorithm
+ Journal: >
+ Proteins: Structure, Function, and Bioinformatics
+ Volume: 64
+ Number: 3
+ Pages: 559-574
+ Year: 2006
+ URL: http://www3.interscience.wiley.com/journal/112638073/abstract
+Watch: http://www.cs.mu.oz.au/~arun/mustang/ ./mustang_v([.\d]*)\.tgz
Added: packages-metadata/n/ncoils.upstream
===================================================================
--- packages-metadata/n/ncoils.upstream (rev 0)
+++ packages-metadata/n/ncoils.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,12 @@
+Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl
+Name: Coils
+Reference:
+ Author: A. Lupas, M. Van Dyke, and J. Stock
+ Title: Predicting coiled coils from protein sequences
+ Journal: Science
+ Volume: 252
+ Pages: 1162-1164
+ Year: 1991
+ DOI: 10.1126/science.252.5009.1162
+ PMID: 2031185
+ URL: http://www.sciencemag.org/content/252/5009/1162
Added: packages-metadata/p/perlprimer.upstream
===================================================================
--- packages-metadata/p/perlprimer.upstream (rev 0)
+++ packages-metadata/p/perlprimer.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Archive: SourceForge
+Contact: http://perlprimer.sourceforge.net/contact.html
+Homepage: http://perlprimer.sourceforge.net
+Name: PerlPrimer
+Reference:
+ author: Marshall, Owen J.
+ title: >
+ PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
+ journal: Bioinformatics
+ volume: 20
+ number: 15
+ pages: 2471-2472
+ doi: 10.1093/bioinformatics/bth254
+ PMID: 15073005
+ year: 2004
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/15/2471
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/20/15/2471.pdf
+Screenshots: http://perlprimer.sourceforge.net/screenshots.html
+Watch: http://sf.net/perlprimer/perlprimer-(.*)\.tar\.bz2
Added: packages-metadata/p/phyml.upstream
===================================================================
--- packages-metadata/p/phyml.upstream (rev 0)
+++ packages-metadata/p/phyml.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,23 @@
+Archive: Google code
+Contact: Stephane Guindon <guindon at stat.auckland.ac.nz>
+Name: PhyML
+Homepage: http://www.atgc-montpellier.fr/phyml
+Reference:
+ author: Guindon, Stephane and Gascuel, Olivier
+ title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
+ journal: Syst Biol
+ volume: 52
+ number: 5
+ pages: 696-704
+ doi: 10.1080/10635150390235520
+ year: 2003
+ URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696
+ eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf
+ PMID: 14530136
+Repository: http://phyml.googlecode.com/svn/trunk/
+Repository-Browse: http://code.google.com/p/phyml/source/browse/
+Watch: |
+ version=3
+ http://code.google.com/p/phyml/downloads/list \
+ http://phyml[.]googlecode[.]com/files/phyml_(20.*)[.]tar[.]gz
+Webservice: http://www.atgc-montpellier.fr/phyml
Added: packages-metadata/p/poa.upstream
===================================================================
--- packages-metadata/p/poa.upstream (rev 0)
+++ packages-metadata/p/poa.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,18 @@
+Contact: Christopher Lee <leec at mbi.ucla.edu>
+Reference-DOI: 10.1093/bioinformatics/bth126
+Homepage: http://www.bioinformatics.ucla.edu/poa
+Name: POA
+Reference-PMID: 14962922
+Reference:
+ author: Grasso, Catherine and Lee, Christopher
+ title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
+ journal: Bioinformatics
+ volume: 20
+ number: 10
+ pages: 1546-1556
+ year: 2004
+ URL: http:°bioinformatics.oxfordjournals.org¢gi¢ontentåbstract½0/10/1546
+ eprint: http:°bioinformatics.oxfordjournals.org¢gi/reprint½0/10/1546.pdf
+Watch: |
+ opts="uversionmangle=s/$/.0/,dversionmangle=s/\+.*$//" \
+ http://sf.net/poamsa/ poaV(.*)\.tar\.gz
Added: packages-metadata/p/primer3.upstream
===================================================================
--- packages-metadata/p/primer3.upstream (rev 0)
+++ packages-metadata/p/primer3.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Contact: Steve Rozen (http://purl.com/STEVEROZEN/)
+Homepage: http://primer3.sourceforge.net
+Name: Primer3
+Reference-PMID: 10547847
+Reference:
+ Author: Steve Rozen and Helen J. Skaletsky
+ Year: 2000
+ Title: Primer3 on the WWW for general users and for biologist programmers
+ Booktitle: >
+ Bioinformatics Methods and Protocols: Methods in Molecular Biology
+ Journal: Methods Mol Biol.
+ Pages: 365-86
+ Number: 132
+ Publisher: Humana Press
+ Editor: Krawetz S, Misener S
+Watch: http://sf.net/primer3/primer3-([\d.]*)\.tar\.gz
+Webservice:
+ - http://frodo.wi.mit.edu/primer3/
+ - http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
Added: packages-metadata/p/probalign.upstream
===================================================================
--- packages-metadata/p/probalign.upstream (rev 0)
+++ packages-metadata/p/probalign.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Usman Roshan <usman at cs.njit.edu>
+Reference-DOI: 10.1093/bioinformatics/btl472
+Homepage: http://cs.njit.edu/usman/probalign/
+Reference-PMID: 16954142
+Name: Probalign
+Reference:
+ AUTHOR: Usman Roshan, Dennis R. Livesay
+ TITILE: >
+ Probalign: multiple sequence alignment using partition function posterior probabilities
+ JOURNAL: Bioinformatics
+ YEAR: 2006
+ PAGES: 2715-21
+ VOLUME: 22
+ NUMBER: 22
+ URL: http://bioinformatics.oxfordjournals.org/content/22/22/2715.short
+ ISSN: 1460-2059
Added: packages-metadata/p/probcons.upstream
===================================================================
--- packages-metadata/p/probcons.upstream (rev 0)
+++ packages-metadata/p/probcons.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Chuong Do <chuongdo at cs.stanford.edu>
+Reference-DOI: 10.1101/gr.2821705
+Homepage: http://probcons.stanford.edu/
+Name: ProbCons
+Reference-PMID: 15687296
+Reference:
+ author: Do, Chuong B. and Mahabhashyam, Mahathi S.P. and Brudno, Michael and Batzoglou, Serafim
+ title: >
+ ProbCons: Probabilistic consistency-based multiple sequence alignment
+ journal: Genome Research
+ volume: 15
+ number: 2
+ pages: 330-340
+ year: 2005
+ URL: http://genome.cshlp.org/content/15/2/330.abstract
+ eprint: http://genome.cshlp.org/content/15/2/330.full.pdf+html
+Watch: http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz
Added: packages-metadata/p/proda.upstream
===================================================================
--- packages-metadata/p/proda.upstream (rev 0)
+++ packages-metadata/p/proda.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Reference-DOI: 10.1093/nar/gkl511
+Name: ProDA
+Homepage: http://proda.stanford.edu/
+Reference-PMID: 17068081
+Reference:
+ author: Phuong, Tu Minh and Do, Chuong B. and Edgar, Robert C. and Batzoglou, Serafim
+ title: Multiple alignment of protein sequences with repeats and rearrangements
+ journal: Nucl. Acids Res.
+ volume: 34
+ number: 20
+ pages: 5932-5942
+ year: 2006
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/34/20/5932
+ eprint: http://nar.oxfordjournals.org/cgi/reprint/34/20/5932.pdf
+Watch: |
+ opts="uversionmangle=s/_/\./" \
+ http://proda.stanford.edu/proda_(.*)\.tar\.gz
Added: packages-metadata/q/qiime.upstream
===================================================================
--- packages-metadata/q/qiime.upstream (rev 0)
+++ packages-metadata/q/qiime.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,12 @@
+Name: QIIME
+Homepage: http://www.qiime.org/
+Reference-DOI: 10.1038/nmeth.f.303
+Reference-PMID: 20383131
+Reference:
+ Author: Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R.
+ Title: QIIME allows analysis of high-throughput community sequencing data
+ Journal: Nature Methods
+ Volume: 7
+ Pages: 335 - 336
+ Year: 2010
+ URL: http://www.nature.com/nmeth/journal/v7/n5/full/nmeth.f.303.html
Added: packages-metadata/r/r-bioc-limma.upstream
===================================================================
--- packages-metadata/r/r-bioc-limma.upstream (rev 0)
+++ packages-metadata/r/r-bioc-limma.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,3 @@
+Archive: Bioconductor
+Homepage: http://bioinf.wehi.edu.au/limma/
+Name: limma
Added: packages-metadata/r/r-cran-epitools.upstream
===================================================================
--- packages-metadata/r/r-cran-epitools.upstream (rev 0)
+++ packages-metadata/r/r-cran-epitools.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,8 @@
+Archive: CRAN
+Contact: Tomas Aragon <aragon at berkeley.edu>
+CRAN: epitools
+Download: http://cran.r-project.org/src/contrib/
+Help: http://groups.yahoo.com/group/epitools/
+Homepage: http://sites.google.com/site/medepi/epitools
+Name: EpiTools
+Watch: http://cran.r-project.org/src/contrib/epitools_([-\d.]*)\.tar\.gz
Added: packages-metadata/r/r-cran-haplo.stats.upstream
===================================================================
--- packages-metadata/r/r-cran-haplo.stats.upstream (rev 0)
+++ packages-metadata/r/r-cran-haplo.stats.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,2 @@
+Contact: Jason P. Sinnwell <sinnwell.jason at mayo.edu>
+Homepage: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
Added: packages-metadata/r/r-cran-qtl.upstream
===================================================================
--- packages-metadata/r/r-cran-qtl.upstream (rev 0)
+++ packages-metadata/r/r-cran-qtl.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,10 @@
+Homepage: http://www.rqtl.org
+Name: "R/qtl: A QTL mapping environment"
+Reference:
+ Author: K. W. Broman, H. Wu, S. Sen, G. A. Churchill
+ Title: >
+ R/qtl: QTL mapping in experimental crosses.
+ Journal: Bioinformatics
+ Number: 19
+ Pages: 889-890
+ Year: 2003
Added: packages-metadata/r/r-cran-qvalue.upstream
===================================================================
--- packages-metadata/r/r-cran-qvalue.upstream (rev 0)
+++ packages-metadata/r/r-cran-qvalue.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Bioconductor: http://www.bioconductor.org/packages/bioc/html/qvalue.html
+Contact: John D. Storey <jstorey at u.washington.edu>
+CRAN: http://cran.r-project.org/web/packages/qvalue/
+Reference-DOI: 10.1073/pnas.1530509100
+Homepage: http://cran.r-project.org/web/packages/qvalue/
+Name: qvalue
+Reference-PMID: 12883005
+Reference:
+ article: John D.Storey08052003
+ author: Storey, John D. and Tibshirani, Robert
+ title: Statistical significance for genomewide studies
+ journal: Proceedings of the National Academy of Sciences of the United States of America
+ volume: 100
+ number: 16
+ pages: 9440-9445
+ doi: 10.1073/pnas.1530509100
+ year: 2003
+ URL: http://www.pnas.org/content/100/16/9440.abstract
+ eprint: http://www.pnas.org/content/100/16/9440.full.pdf+html
Added: packages-metadata/r/r-cran-randomforest.upstream
===================================================================
--- packages-metadata/r/r-cran-randomforest.upstream (rev 0)
+++ packages-metadata/r/r-cran-randomforest.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,5 @@
+Archive: http://cran.r-project.org/src/contrib/Archive/randomForest/
+Contact: Andy Liaw <andy_liaw at merck.com>
+CRAN: RandomForest
+Homepage: http://cran.r-project.org/web/packages/randomForest/
+Name: RandomForest
Added: packages-metadata/r/r-cran-rocr.upstream
===================================================================
--- packages-metadata/r/r-cran-rocr.upstream (rev 0)
+++ packages-metadata/r/r-cran-rocr.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,22 @@
+Contact:
+ - Tobias Sing <tobias.sing at mpi-sb.mpg.de>
+ - Oliver Sander <osander at mpi-sb.mpg.de>
+Reference-DOI: 10.1093/bioinformatics/bti623
+Gallery: http://rocr.bioinf.mpi-sb.mpg.de/rocr_gallery.html
+Homepage: http://rocr.bioinf.mpi-sb.mpg.de
+Name: ROCR
+Reference-PMID: 16096348
+Reference: |
+ author: Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas
+ title: ROCR: visualizing classifier performance in R
+ journal: Bioinformatics
+ volume: 21
+ number: 20
+ pages: 3940-3941
+ year: 2005
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/20/3940
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/21/20/3940.pdf
+Screenshot:
+ - http://rocr.bioinf.mpi-sb.mpg.de/plot1.jpg
+ - http://rocr.bioinf.mpi-sb.mpg.de/plot.jpg
+Watch: http://cran.r-project.org/src/contrib/ROCR_([-0-9\.]*)\.tar\.gz
Added: packages-metadata/r/r-other-bio3d.upstream
===================================================================
--- packages-metadata/r/r-other-bio3d.upstream (rev 0)
+++ packages-metadata/r/r-other-bio3d.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Contact: Barry Grant <bgrant at mccammon.ucsd.edu>
+Reference-DOI: 10.1093/bioinformatics/btl461
+Gallery: http://mccammon.ucsd.edu/~bgrant/bio3d/gallery/gallery.html
+Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/
+Name: Bio3D
+Reference-PMID: 16940322
+Reference:
+ author: Grant, Barry J. and Rodrigues, Ana P. C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S. D.
+ title: >
+ Bio3d: an R package for the comparative analysis of protein structures
+ journal: Bioinformatics
+ volume: 22
+ number: 21
+ pages: 2695-2696
+ doi: 10.1093/bioinformatics/btl461
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2695
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/21/2695.pdf
+Wiki: http://bio3d.pbworks.com/
Added: packages-metadata/r/r-other-mott-happy.upstream
===================================================================
--- packages-metadata/r/r-other-mott-happy.upstream (rev 0)
+++ packages-metadata/r/r-other-mott-happy.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,15 @@
+Contact: Richard Mott <Richard.Mott at well.ox.ac.uk>
+Reference-DOI: 10.1073/pnas.230304397
+Homepage: http://www.well.ox.ac.uk/happy/happyR
+Name: HAPPY
+Reference-PMID: 11050180
+Reference:
+ author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan
+ title: A method for fine mapping quantitative trait loci in outbred animal stocks
+ journal: Proc Natl Acad Sci U S A
+ volume: 97
+ number: 23
+ pages: 12649-12654
+ year: 2000
+ URL: http://www.pnas.org/content/97/23/12649.abstract
+ eprint: http://www.pnas.org/content/97/23/12649.full.pdf+html
Added: packages-metadata/r/raster3d.upstream
===================================================================
--- packages-metadata/r/raster3d.upstream (rev 0)
+++ packages-metadata/r/raster3d.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,11 @@
+Homepage: http://skuld.bmsc.washington.edu/raster3d/
+Name: Raster3D
+Reference-PMID: 18488322
+Reference:
+ Article: MerrittBacon1997
+ Author: Merritt, E.A. and Bacon, D.J.
+ Title: Raster3D Photorealistic Molecular Graphics
+ Journal: Methods in Enzymology
+ Volume: 277
+ Pages: 505-524
+ Year: 1997
Added: packages-metadata/r/raxml.upstream
===================================================================
--- packages-metadata/r/raxml.upstream (rev 0)
+++ packages-metadata/r/raxml.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,12 @@
+Contact: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+Reference-DOI: 10.1093/bioinformatics/btl446
+Homepage: http://wwwkramer.in.tum.de/exelixis/software.html
+Name: RAxML
+Reference-PMID: 16928733
+Reference:
+ author: 16928733
+ title: >
+ RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
+ journal: Bioinformatics
+ year: 2006
+ URL: http://bioinformatics.oxfordjournals.org/content/22/21/2688.full
Added: packages-metadata/r/rnahybrid.upstream
===================================================================
--- packages-metadata/r/rnahybrid.upstream (rev 0)
+++ packages-metadata/r/rnahybrid.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Reference-DOI: 10.1261/rna.5248604
+Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
+Name: RNAhybrid
+Reference-PMID: 15383676
+Reference:
+ author: REHMSMEIER, MARC and STEFFEN, PETER and HÖCHSMANN, MATTHIAS and GIEGERICH, ROBERT
+ title: Fast and effective prediction of microRNA/target duplexes
+ journal: RNA
+ volume: 10
+ number: 10
+ pages: 1507-1517
+ doi: 10.1261/rna.5248604
+ year: 2004
+ URL: http://rnajournal.cshlp.org/content/10/10/1507.abstract
+ eprint: http://rnajournal.cshlp.org/content/10/10/1507.full.pdf+html
+Webservice: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html
Added: packages-metadata/s/samtools.upstream
===================================================================
--- packages-metadata/s/samtools.upstream (rev 0)
+++ packages-metadata/s/samtools.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,18 @@
+Archive: SourceForge
+Homepage: http://samtools.sourceforge.net
+mr:
+ checkout: debcheckout -a git://git.debian.org/debian-med/samtools.git
+Name: SAM tools
+Reference:
+ author: Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup
+ title: The Sequence Alignment/Map (SAM) Format and SAMtools
+ journal: Bioinformatics
+ volume: 25
+ number: 16
+ pages: 2078-2079
+ doi: 10.1093/bioinformatics/btp352
+ PMID: 19505943
+ year: 2009
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp352v1
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf
+Repository: https://samtools.svn.sourceforge.net/svnroot/samtools
Added: packages-metadata/s/seaview.upstream
===================================================================
--- packages-metadata/s/seaview.upstream (rev 0)
+++ packages-metadata/s/seaview.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,21 @@
+Contact: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+Documentation: http://pbil.univ-lyon1.fr/software/seaview_data/seaview
+Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
+Homepage: http://pbil.univ-lyon1.fr/software/seaview
+Name: SeaView
+Reference:
+ author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
+ title: >
+ SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building
+ journal: Mol Biol Evol
+ volume: 27
+ number: 2
+ pages: 221-224
+ year: 2010
+ PMID: 19854763
+ DOI: 10.1093/molbev/msp259
+ URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221
+ eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf
+Screenshots:
+ - http://pbil.univ-lyon1.fr/binaries/seaview4.png
+ - http://pbil.univ-lyon1.fr/binaries/seaview-tree.png
Added: packages-metadata/s/seqan-apps.upstream
===================================================================
--- packages-metadata/s/seqan-apps.upstream (rev 0)
+++ packages-metadata/s/seqan-apps.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,20 @@
+Contact: SeqAn Team (http://www.seqan.de/contact-us.html)
+Reference-DOI: 10.1186/1471-2105-9-11
+Donate: http://www.seqan.de/
+Homepage: http://www.seqan.de/
+Name: SeqAn
+Reference-PMID: 18184432
+Reference:
+ AUTHOR: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut
+ TITLE: SeqAn An efficient, generic C++ library for sequence analysis
+ JOURNAL: BMC Bioinformatics
+ VOLUME: 9
+ YEAR: 2008
+ NUMBER: 1
+ PAGES: 11
+ URL: http://www.biomedcentral.com/1471-2105/9/11
+ ISSN: 1471-2105
+Watch: |
+ http://www.seqan.de/downloads/releases.html \
+ .*/Seqan_Release_([\d\.]+).zip \
+ debian debian/orig-tar.sh
Added: packages-metadata/s/seqan-dev.upstream
===================================================================
--- packages-metadata/s/seqan-dev.upstream (rev 0)
+++ packages-metadata/s/seqan-dev.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,20 @@
+Contact: SeqAn Team (http://www.seqan.de/contact-us.html)
+Reference-DOI: 10.1186/1471-2105-9-11
+Donate: http://www.seqan.de/
+Homepage: http://www.seqan.de/
+Name: SeqAn
+Reference-PMID: 18184432
+Reference:
+ AUTHOR: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut
+ TITLE: SeqAn An efficient, generic C++ library for sequence analysis
+ JOURNAL: BMC Bioinformatics
+ VOLUME: 9
+ YEAR: 2008
+ NUMBER: 1
+ PAGES: 11
+ URL: http://www.biomedcentral.com/1471-2105/9/11
+ ISSN: 1471-2105
+Watch: |
+ http://www.seqan.de/downloads/releases.html \
+ .*/Seqan_Release_([\d\.]+).zip \
+ debian debian/orig-tar.sh
Added: packages-metadata/s/sigma-align.upstream
===================================================================
--- packages-metadata/s/sigma-align.upstream (rev 0)
+++ packages-metadata/s/sigma-align.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Rahul Siddharthan <rsidd AT imsc.res.in>
+Reference-DOI: 10.1186/1471-2105-7-143
+Homepage: http://www.imsc.res.in/~rsidd/sigma/
+Reference-PMID: 16542424
+Name: Sigma
+Reference:
+ AUTHOR: Siddharthan, Rahul
+ TITLE: >
+ Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
+ JOURNAL: BMC Bioinformatics
+ VOLUME: 7
+ YEAR: 2006
+ NUMBER: 1
+ PAGES: 143
+ URL: http://www.biomedcentral.com/1471-2105/7/143
+ ISSN: 1471-2105
+Watch: http://www.imsc.res.in/~rsidd/sigma/ source/sigma-(.*)\.tar\.gz
Added: packages-metadata/s/ssake.upstream
===================================================================
--- packages-metadata/s/ssake.upstream (rev 0)
+++ packages-metadata/s/ssake.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,19 @@
+Homepage: http://www.bcgsc.ca/platform/bioinfo/software/ssake
+Name: SSAKE
+Reference:
+ author: Warren, Rene L. and Sutton, Granger G. and Jones, Steven J. M. and Holt, Robert A.
+ title: Assembling millions of short DNA sequences using SSAKE
+ journal: Bioinformatics
+ volume: 23
+ number: 4
+ pages: 500-501
+ doi: 10.1093/bioinformatics/btl629
+ PMID: 17158514
+ year: 2007
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/4/500
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/4/500.pdf
+Watch: |
+ version=3
+
+ opts="uversionmangle=s/-/\./g" \
+ http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/([\d.]*)/ssake_v([-\d]*)-tar.gz
Added: packages-metadata/t/t-coffee.upstream
===================================================================
--- packages-metadata/t/t-coffee.upstream (rev 0)
+++ packages-metadata/t/t-coffee.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Cédric Notredame <cedric.notredame at europe.com>
+Reference-DOI: 10.1006/jmbi.2000.4042
+Name: T-Coffee
+Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+Reference-PMID: 10964570
+Reference-Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa
+Reference-Journal: Journal of Molecular Biology
+Reference-Number: 1
+Reference-Pages: 205-217
+Reference-Title: >
+ T-coffee: a novel method for fast and accurate multiple sequence alignment
+Reference-URL: http://www.sciencedirect.com/science/article/B6WK7-45F5150-7S/2/9c2fd0f2a43f877fd801b3245fe0beed
+Reference-Volume: 302
+Reference-Year: 2000
+Watch: http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz
+Webservice: http://tcoffee.crg.cat/apps/tcoffee/do:regular
Added: packages-metadata/t/tm-align.upstream
===================================================================
--- packages-metadata/t/tm-align.upstream (rev 0)
+++ packages-metadata/t/tm-align.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,16 @@
+Contact: Yang Zhang <zhng at umich.edu>
+Reference-DOI: 10.1093/nar/gki524
+Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
+Reference-PMID: 15849316
+Name: TM-align & TM-score
+Reference:
+ AUTHOR: Y. Zhang, J. Skolnick
+ TITILE: >
+ TM-align: A protein structure alignment algorithm based on TM-score
+ JOURNAL: Nucleic Acids Research
+ YEAR: 2005
+ PAGES: 2302-2309
+ VOLUME: 33
+ NUMBER: 7
+ URL: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
+ ISSN: 1362-4962
Added: packages-metadata/t/tophat.upstream
===================================================================
--- packages-metadata/t/tophat.upstream (rev 0)
+++ packages-metadata/t/tophat.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,17 @@
+Contact: Cole Trapnell <cole at cs.umd.edu>
+Homepage: http://tophat.cbcb.umd.edu/
+Name: TopHat
+Reference:
+ author: Cole Trapnell1, Lior Pachter and Steven L. Salzberg
+ title: >
+ TopHat: discovering splice junctions with RNA-Seq
+ journal: Bioinformatics
+ volume: 25
+ number: 9
+ pages: 1105-1111
+ year: 2009
+ DOI: 10.1093/bioinformatics/btp120
+ PMID: 19289445
+ URL: http://bioinformatics.oxfordjournals.org/content/25/9/1105.short
+ eprint: http://bioinformatics.oxfordjournals.org/content/25/9/1105.full.pdf+html
+ license: Open Access
Added: packages-metadata/t/transtermhp.upstream
===================================================================
--- packages-metadata/t/transtermhp.upstream (rev 0)
+++ packages-metadata/t/transtermhp.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,11 @@
+Contact: Carl Kingsford <carlk at umiacs.umd.edu>
+Reference-DOI: 10.1186/gb-2007-8-2-r22
+Homepage: http://transterm.cbcb.umd.edu/
+Reference-PMID: 17313685
+Name: TransTermHP
+Reference:
+ AUTHOR: C. Kingsford, K. Ayanbule, S.L. Salzberg
+ TITILE: Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
+ JOURNAL: Genome Biology
+ YEAR: 2007
+ URL: http://genomebiology.com/2007/8/2/R22/abstract
Added: packages-metadata/t/treeviewx.upstream
===================================================================
--- packages-metadata/t/treeviewx.upstream (rev 0)
+++ packages-metadata/t/treeviewx.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,20 @@
+Archive: Google Code
+Contact: Roderic D. M. Page <r.page at bio.gla.ac.uk>
+Download: http://code.google.com/p/treeviewx/downloads/
+Homepage: http://code.google.com/p/treeviewx/
+Name: Treeview X
+Reference:
+ Author: Page, Roderic D. M.
+ Journal: Comput. Appl. Biosci.
+ Number: 4
+ Page: 357-8
+ Title: >
+ TreeView: an application to display phylogenetic trees on personal computers
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/citation/12/4/357
+ Volume: 12
+ Year: 1996
+ PMID: 8902363
+ DOI: 10.1093/bioinformatics/12.4.357
+Repository: http://treeviewx.googlecode.com/svn/
+Repository-Browse: http://code.google.com/p/treeviewx/source/browse/
+Watch: http://googlecode.debian.net/p/treeviewx/tv.(\d+.*)\.tar\.gz
Added: packages-metadata/v/velvet.upstream
===================================================================
--- packages-metadata/v/velvet.upstream (rev 0)
+++ packages-metadata/v/velvet.upstream 2012-03-06 14:42:56 UTC (rev 2170)
@@ -0,0 +1,18 @@
+Contact: Daniel Zerbino <zerbino at ebi.ac.uk>
+Reference-DOI: 10.1101/gr.074492.107
+Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
+Name: Velvet
+Reference-PMID: 18349386
+Reference:
+ author: Zerbino, Daniel R. and Birney, Ewan
+ title: >
+ Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
+ journal: Genome Research
+ volume: 18
+ number: 5
+ pages: 821-829
+ year: 2008
+ URL: http://genome.cshlp.org/content/18/5/821.abstract
+ eprint: http://genome.cshlp.org/content/18/5/821.full.pdf+html
+Repository: http://github.com/dzerbino/velvet
+Watch: http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz
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