Sat Feb 18 01:23:40 UTC 2012

Author: plessy
Date: 2012-02-18 01:23:39 +0000 (Sat, 18 Feb 2012)
New Revision: 9702

Modified:
   trunk/packages/R/r-cran-qvalue/trunk/debian/upstream
   trunk/packages/R/r-cran-rocr/trunk/debian/upstream
   trunk/packages/R/r-other-bio3d/trunk/debian/upstream
   trunk/packages/R/r-other-mott-happy/trunk/debian/upstream
   trunk/packages/adun.app/trunk/debian/upstream
   trunk/packages/alien-hunter/trunk/debian/upstream
   trunk/packages/altree/trunk/debian/upstream
   trunk/packages/autodock-vina/trunk/debian/upstream
   trunk/packages/autodocksuite/trunk/debian/upstream
   trunk/packages/biomaj/trunk/debian/upstream
   trunk/packages/bioperl/trunk/debian/upstream
   trunk/packages/blat/trunk/debian/upstream
   trunk/packages/cd-hit/trunk/debian/upstream
   trunk/packages/circos/trunk/debian/upstream
   trunk/packages/clonalframe/trunk/debian/upstream
   trunk/packages/clustalo/trunk/debian/upstream
   trunk/packages/coils/trunk/debian/upstream
   trunk/packages/dialign-t/trunk/debian/upstream
   trunk/packages/dialign/trunk/debian/upstream
   trunk/packages/epigrass/trunk/debian/upstream
   trunk/packages/exonerate/trunk/debian/upstream
   trunk/packages/gassst/trunk/debian/upstream
   trunk/packages/glam2/trunk/debian/upstream
   trunk/packages/hmmer/trunk/debian/upstream
   trunk/packages/infernal/trunk/debian/upstream
   trunk/packages/kalign/trunk/debian/upstream
   trunk/packages/last-align/trunk/debian/upstream
   trunk/packages/libhmsbeagle/trunk/debian/upstream
   trunk/packages/libtfbs-perl/trunk/debian/upstream
   trunk/packages/mafft/trunk/debian/upstream
   trunk/packages/maq/trunk/debian/upstream
   trunk/packages/maude/trunk/debian/upstream
   trunk/packages/melting/trunk/debian/upstream
   trunk/packages/mgltools/autodocktools/trunk/debian/upstream
   trunk/packages/mothur/trunk/debian/upstream
   trunk/packages/mustang/trunk/debian/upstream
   trunk/packages/phy-spread/trunk/debian/upstream
   trunk/packages/poa/trunk/debian/upstream
   trunk/packages/primer3/trunk/debian/upstream
   trunk/packages/probalign/trunk/debian/upstream
   trunk/packages/probcons/trunk/debian/upstream
   trunk/packages/proda/trunk/debian/upstream
   trunk/packages/python-pynast/trunk/debian/upstream
   trunk/packages/qiime/trunk/debian/upstream
   trunk/packages/raster3d/trunk/debian/upstream
   trunk/packages/raxml/trunk/debian/upstream
   trunk/packages/rnahybrid/trunk/debian/upstream
   trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream
   trunk/packages/rostlab/libzerg/trunk/debian/upstream
   trunk/packages/seqan/trunk/debian/upstream
   trunk/packages/sigma-align/trunk/debian/upstream
   trunk/packages/t-coffee/trunk/debian/upstream
   trunk/packages/tm-align/trunk/debian/upstream
   trunk/packages/transtermhp/trunk/debian/upstream
   trunk/packages/velvet/trunk/debian/upstream
Log:
debian/upstream: Moved DOI and PMID to the Reference namespace.


Modified: trunk/packages/R/r-cran-qvalue/trunk/debian/upstream
===================================================================

--- trunk/packages/R/r-cran-qvalue/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,10 +1,10 @@
 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/
-DOI: 10.1073/pnas.1530509100
+Reference-DOI: 10.1073/pnas.1530509100
 Homepage: http://cran.r-project.org/web/packages/qvalue/
 Name: qvalue
-PMID: 12883005
+Reference-PMID: 12883005
 Reference:
  article: John D.Storey08052003
  author: Storey, John D. and Tibshirani, Robert

Modified: trunk/packages/R/r-cran-rocr/trunk/debian/upstream
===================================================================
--- trunk/packages/R/r-cran-rocr/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/R/r-cran-rocr/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,11 +1,11 @@
 Contact:
  - Tobias Sing <tobias.sing at mpi-sb.mpg.de>
  - Oliver Sander <osander at mpi-sb.mpg.de>
-DOI: 10.1093/bioinformatics/bti623
+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
-PMID: 16096348
+Reference-PMID: 16096348
 Reference: |
  author: Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas
  title: ROCR: visualizing classifier performance in R

Modified: trunk/packages/R/r-other-bio3d/trunk/debian/upstream
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,9 +1,9 @@
 Contact: Barry Grant <bgrant at mccammon.ucsd.edu>
-DOI: 10.1093/bioinformatics/btl461
+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
-PMID: 16940322
+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

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/upstream
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Richard Mott <Richard.Mott at well.ox.ac.uk>
-DOI: 10.1073/pnas.230304397
+Reference-DOI: 10.1073/pnas.230304397
 Homepage: http://www.well.ox.ac.uk/happy/happyR
 Name: HAPPY
-PMID: 11050180
+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

Modified: trunk/packages/adun.app/trunk/debian/upstream
===================================================================
--- trunk/packages/adun.app/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/adun.app/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Archive: Gna
-DOI: 10.1002/jcc.20312
+Reference-DOI: 10.1002/jcc.20312
 Homepage: http://diana.imim.es/Adun
 Name: Adun
-PMID: 16175583
+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

Modified: trunk/packages/alien-hunter/trunk/debian/upstream
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/alien-hunter/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact   : George Vernikos <gsv at sanger.ac.uk>
-DOI: 10.1093/bioinformatics/btl369
+Reference-DOI: 10.1093/bioinformatics/btl369
 Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html
 Name: Alien_hunter
-PMID: 16837528
+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

Modified: trunk/packages/altree/trunk/debian/upstream
===================================================================
--- trunk/packages/altree/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/altree/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Claire Bardel <Claire.Bardel at univ-lyon1.fr>
-DOI: 10.1093/bioinformatics/btl131
+Reference-DOI: 10.1093/bioinformatics/btl131
 Homepage: http://claire.bardel.free.fr/software.html
 Name: ALTree
-PMID: 16595555
+Reference-PMID: 16595555
 Reference-Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle
 Reference-Journal: Bioinformatics
 Reference-Number: 11

Modified: trunk/packages/autodock-vina/trunk/debian/upstream
===================================================================
--- trunk/packages/autodock-vina/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/autodock-vina/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,5 +1,5 @@
 Contact: Oleg Trott <ot14 at columbia.edu>
-DOI: 10.1002/jcc.21334
+Reference-DOI: 10.1002/jcc.21334
 Homepage: http://vina.scripps.edu
 Name: AutoDock Vina
 Reference:

Modified: trunk/packages/autodocksuite/trunk/debian/upstream
===================================================================
--- trunk/packages/autodocksuite/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/autodocksuite/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
-DOI: 10.1002/jcc.21256
+Reference-DOI: 10.1002/jcc.21256
 Homepage: http://autodock.scripps.edu/
 Name: AutoDock
-PMID: 19399780
+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

Modified: trunk/packages/biomaj/trunk/debian/upstream
===================================================================
--- trunk/packages/biomaj/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/biomaj/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,4 +1,4 @@
-DOI: 10.1093/bioinformatics/btn325
+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

Modified: trunk/packages/bioperl/trunk/debian/upstream
===================================================================
--- trunk/packages/bioperl/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/bioperl/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,9 +1,9 @@
 Bug-Database: https://redmine.open-bio.org/projects/bioperl
 Contact: Bioperl developers <bioperl-l at bioperl.org>
-DOI: 10.1101/gr.361602
+Reference-DOI: 10.1101/gr.361602
 Homepage: http://www.bioperl.org/
 Name: BioPerl
-PMID: 12368254
+Reference-PMID: 12368254
 Reference: 
    author: >
         J.E. Stajich and D. Block and K. Boulez and S.E. Brenner

Modified: trunk/packages/blat/trunk/debian/upstream
===================================================================
--- trunk/packages/blat/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/blat/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,12 +1,12 @@
 NAME: BLAT
 Reference:
- author = Kent, W. James
- title = BLAT—The BLAST-Like Alignment Tool
- journal = Genome Research
- volume = 12
- number = 4
- pages = 656-664
- doi = 10.1101/gr.229202
- year = 2002
- URL = http://genome.cshlp.org/content/12/4/656.abstract
- eprint = http://genome.cshlp.org/content/12/4/656.full.pdf+html
+ author: Kent, W. James
+ title: BLAT—The BLAST-Like Alignment Tool
+ journal: Genome Research
+ volume: 12
+ number: 4
+ pages: 656-664
+ doi: 10.1101/gr.229202
+ year: 2002
+ URL: http://genome.cshlp.org/content/12/4/656.abstract
+ eprint: http://genome.cshlp.org/content/12/4/656.full.pdf+html

Modified: trunk/packages/cd-hit/trunk/debian/upstream
===================================================================
--- trunk/packages/cd-hit/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/cd-hit/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Weizhong Li <liwz at sdsc.edu>
-DOI: 10.1093/bioinformatics/btl158
+Reference-DOI: 10.1093/bioinformatics/btl158
 Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
 Name: CD-HIT
-PMID: 16731699
+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.

Modified: trunk/packages/circos/trunk/debian/upstream
===================================================================
--- trunk/packages/circos/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/circos/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,4 +1,4 @@
-DOI: 10.1101/gr.092759.109
+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

Modified: trunk/packages/clonalframe/trunk/debian/upstream
===================================================================
--- trunk/packages/clonalframe/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/clonalframe/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,5 +1,5 @@
 Contact: Xavier Didelot <xavier.didelot at gmail.com>
-DOI: 10.1534/genetics.106.063305
+Reference-DOI: 10.1534/genetics.106.063305
 Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
 Name: ClonalFrame
 Reference:

Modified: trunk/packages/clustalo/trunk/debian/upstream
===================================================================
--- trunk/packages/clustalo/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/clustalo/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Fabian Sievers (UCD Dublin, Ireland)
-DOI: 10.1038/msb.2011.75
+Reference-DOI: 10.1038/msb.2011.75
 Homepage: http://www.clustal.org/omega/
 Name: Clustal Omega
-PMID: 21988835
+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

Modified: trunk/packages/coils/trunk/debian/upstream
===================================================================
--- trunk/packages/coils/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/coils/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,6 +1,6 @@
 Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl
 Name: Coils
-PMID: 2031185
+Reference-PMID: 2031185
 Reference:
  Author: A. Lupas, M. Van Dyke, and J. Stock
  Title: Predicting coiled coils from protein sequences

Modified: trunk/packages/dialign/trunk/debian/upstream
===================================================================
--- trunk/packages/dialign/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/dialign/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
-DOI: 10.1093/bioinformatics/15.3.211
+Reference-DOI: 10.1093/bioinformatics/15.3.211
 Name: DIALIGN
 Homepage: http://dialign.gobics.de/
-PMID: 10222408
+Reference-PMID: 10222408
 Reference:
  Author: Morgenstern, B
  Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment

Modified: trunk/packages/dialign-t/trunk/debian/upstream
===================================================================
--- trunk/packages/dialign-t/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/dialign-t/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
-DOI: 10.1186/1748-7188-3-6
+Reference-DOI: 10.1186/1748-7188-3-6
 Homepage: http://dialign-tx.gobics.de/
-PMID: 18505568
+Reference-PMID: 18505568
 Name: DIALIGN-T
 Reference:
  AUTHOR: Subramanian, Amarendran and Kaufmann, Michael and Morgenstern, Burkhard

Modified: trunk/packages/epigrass/trunk/debian/upstream
===================================================================
--- trunk/packages/epigrass/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/epigrass/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,18 +1,16 @@
 Contact:  Flavio Codeco Coelho <fccoelho at gmail.com>
-DOI:      10.1186/1751-0473-3-3
 Homepage: http://epigrass.sourceforge.net/
 Name:     EpiGrass
 Watch:    http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz
-PMID:     18302744
 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
-}
-

Modified: trunk/packages/exonerate/trunk/debian/upstream
===================================================================
--- trunk/packages/exonerate/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/exonerate/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Guy St.C. Slater <guy AT ebi.ac.uk>
-DOI: 10.1186/1471-2105-6-31
+Reference-DOI: 10.1186/1471-2105-6-31
 Name: Exonerate
 Homepage: http://www.ebi.ac.uk/~guy/exonerate/
-PMID: 15713233
+Reference-PMID: 15713233
 Reference:
  Author: Slater, Guy and Birney, Ewan
  Title: Automated generation of heuristics for biological sequence comparison

Modified: trunk/packages/gassst/trunk/debian/upstream
===================================================================
--- trunk/packages/gassst/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/gassst/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,5 +1,5 @@
 Contact: Dominique Lavanier <dominique.lavanier at irisa.fr>
-DOI: 10.1093/bioinformatics/btq485
+Reference-DOI: 10.1093/bioinformatics/btq485
 Homepage: http://www.irisa.fr/symbiose/projects/gassst/
 Name: GASSST
 Reference:

Modified: trunk/packages/glam2/trunk/debian/upstream
===================================================================
--- trunk/packages/glam2/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/glam2/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Martin C Frith <martin at cbrc.jp> and Timothy L Bailey <t.bailey at imb.uq.edu.au>
-DOI: 10.1371/journal.pcbi.1000071
+Reference-DOI: 10.1371/journal.pcbi.1000071
 Homepage: http://bioinformatics.org.au/glam2/
 Name: GLAM2
-PMID: 18437229
+Reference-PMID: 18437229
 Reference:
  author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.
  journal: PLoS Comput Biol

Modified: trunk/packages/hmmer/trunk/debian/upstream
===================================================================
--- trunk/packages/hmmer/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/hmmer/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: http://selab.janelia.org/people/eddys/contact.html
-DOI: 10.1093/bioinformatics/14.9.755
+Reference-DOI: 10.1093/bioinformatics/14.9.755
 Name: HMMER
 Homepage: http://hmmer.janelia.org
-PMID: 9918945
+Reference-PMID: 9918945
 Reference:
   Author: Eddy, SR
   Title: Profile hidden Markov models

Modified: trunk/packages/infernal/trunk/debian/upstream
===================================================================
--- trunk/packages/infernal/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/infernal/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,6 +1,6 @@
-DOI: 10.1093/bioinformatics/btp157
+Reference-DOI: 10.1093/bioinformatics/btp157
 Homepage: http://infernal.janelia.org/
-PMID: 19307242
+Reference-PMID: 19307242
 Reference: 
  author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
  title: Infernal 1.0: inference of RNA alignments

Modified: trunk/packages/kalign/trunk/debian/upstream
===================================================================
--- trunk/packages/kalign/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/kalign/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Timo Lassmann <timolassmann at gmail.com>
-DOI: 10.1093/nar/gkn1006
+Reference-DOI: 10.1093/nar/gkn1006
 Name: Kalign
 Homepage: http://msa.cgb.ki.se
-PMID: 19103665
+Reference-PMID: 19103665
 Reference:
   Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.
   Journal: Nucl. Acids Res.

Modified: trunk/packages/last-align/trunk/debian/upstream
===================================================================
--- trunk/packages/last-align/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/last-align/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: last (ATmark) cbrc (dot) jp
-DOI: 10.1093/nar/gkq010
+Reference-DOI: 10.1093/nar/gkq010
 Name: LAST
 Homepage: http://last.cbrc.jp/
-PMID: 20110255
+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

Modified: trunk/packages/libhmsbeagle/trunk/debian/upstream
===================================================================
--- trunk/packages/libhmsbeagle/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/libhmsbeagle/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Andrew Rambaut <rambaut at gmail.com>
-DOI: 10.1093/sysbio/syr100
+Reference-DOI: 10.1093/sysbio/syr100
 Homepage:  http://code.google.com/p/beagle-lib
 Name: beagle-lib
-PMID: 21963610
+Reference-PMID: 21963610
 Reference:
   author: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard
   title: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

Modified: trunk/packages/libtfbs-perl/trunk/debian/upstream
===================================================================
--- trunk/packages/libtfbs-perl/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/libtfbs-perl/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Boris.Lenhard at bccs.uib.no
-DOI: 10.1093/bioinformatics/18.8.1135
+Reference-DOI: 10.1093/bioinformatics/18.8.1135
 Homepage: http://tfbs.genereg.net/
 Name: TFBS
-PMID: 12176838
+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.

Modified: trunk/packages/mafft/trunk/debian/upstream
===================================================================
--- trunk/packages/mafft/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/mafft/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
-DOI: 10.1093/bib/bbn013
+Reference-DOI: 10.1093/bib/bbn013
 Name: MAFFT
 Homepage: http://mafft.cbrc.jp/alignment/software/
-PMID: 18372315
+Reference-PMID: 18372315
 Reference-Author: Katoh, Kazutaka and Toh, Hiroyuki
 Reference-Journal: Brief Bioinform
 Reference-Number: 4

Modified: trunk/packages/maq/trunk/debian/upstream
===================================================================
--- trunk/packages/maq/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/maq/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,10 +1,10 @@
 Archive: SourceForge
 Contact: Heng Li <lh3 at sanger.ac.uk>
-DOI: 10.1101/gr.078212.108
+Reference-DOI: 10.1101/gr.078212.108
 FAQ: http://maq.sourceforge.net/faq.shtml
 Name: Maq
 Homepage: http://maq.sourceforge.net/
-PMID: 18714091
+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

Modified: trunk/packages/maude/trunk/debian/upstream
===================================================================
--- trunk/packages/maude/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/maude/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,5 +1,5 @@
 Contact: Richard J. Wagner
-DOI: 10.1145/272991.272995
+Reference-DOI: 10.1145/272991.272995
 Homepage: http://www-personal.umich.edu/~wagnerr/MersenneTwister.html
 Name: Mersenne Twister Random Number Generator
 Reference:

Modified: trunk/packages/melting/trunk/debian/upstream
===================================================================
--- trunk/packages/melting/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/melting/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
-DOI: 10.1093/bioinformatics/17.12.1226
+Reference-DOI: 10.1093/bioinformatics/17.12.1226
 Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
 Name: MELTING
-PMID: 11751232
+Reference-PMID: 11751232
 Reference:
  author: Le Novère, Nicolas
  title: MELTING, computing the melting temperature of nucleic acid duplex

Modified: trunk/packages/mgltools/autodocktools/trunk/debian/upstream
===================================================================
--- trunk/packages/mgltools/autodocktools/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/mgltools/autodocktools/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
-DOI: 10.1002/jcc.21256
+Reference-DOI: 10.1002/jcc.21256
 Homepage: http://autodock.scripps.edu/
 Name: AutoDockTools
-PMID: 19399780
+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

Modified: trunk/packages/mothur/trunk/debian/upstream
===================================================================
--- trunk/packages/mothur/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/mothur/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Patrick D. Schloss <pschloss at umich.edu>
-DOI: 10.1128/AEM.01541-09
+Reference-DOI: 10.1128/AEM.01541-09
 Homepage: http://www.mothur.org
-PMID: 19801464
+Reference-PMID: 19801464
 Name: Mothur
 Reference:
  AUTHOR: Schloss, P.D., et al.

Modified: trunk/packages/mustang/trunk/debian/upstream
===================================================================
--- trunk/packages/mustang/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/mustang/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun)
-DOI: 10.1002/prot.20921
+Reference-DOI: 10.1002/prot.20921
 Homepage: http://www.cs.mu.oz.au/~arun/mustang/
 Name: MUSTANG
-PMID: 16736488
+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

Modified: trunk/packages/phy-spread/trunk/debian/upstream
===================================================================
--- trunk/packages/phy-spread/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/phy-spread/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Filip Bielejec <filip.bielejec at rega.kuleuven.be>
-DOI: 10.1093/bioinformatics/btr481
+Reference-DOI: 10.1093/bioinformatics/btr481
 Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
 Name: SPREAD
-PMID: 21911333
+Reference-PMID: 21911333
 Reference:
   author: Filip Bielejec, Andrew Rambaut, Marc A. Suchard and Philippe Lemey
   title: SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

Modified: trunk/packages/poa/trunk/debian/upstream
===================================================================
--- trunk/packages/poa/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/poa/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Christopher Lee <leec at mbi.ucla.edu>
-DOI: 10.1093/bioinformatics/bth126
+Reference-DOI: 10.1093/bioinformatics/bth126
 Homepage: http://www.bioinformatics.ucla.edu/poa
 Name: POA
-PMID: 14962922
+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

Modified: trunk/packages/primer3/trunk/debian/upstream
===================================================================
--- trunk/packages/primer3/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/primer3/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Steve Rozen (http://purl.com/STEVEROZEN/)
 Homepage: http://primer3.sourceforge.net
 Name: Primer3
-PMID: 10547847
+Reference-PMID: 10547847
 Reference:
  Author: Steve Rozen and Helen J. Skaletsky
  Year: 2000

Modified: trunk/packages/probalign/trunk/debian/upstream
===================================================================
--- trunk/packages/probalign/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/probalign/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Usman Roshan <usman at cs.njit.edu>
-DOI: 10.1093/bioinformatics/btl472
+Reference-DOI: 10.1093/bioinformatics/btl472
 Homepage: http://cs.njit.edu/usman/probalign/
-PMID: 16954142
+Reference-PMID: 16954142
 Name: Probalign
 Reference:
  AUTHOR: Usman Roshan, Dennis R. Livesay

Modified: trunk/packages/probcons/trunk/debian/upstream
===================================================================
--- trunk/packages/probcons/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/probcons/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Chuong Do <chuongdo at cs.stanford.edu>
-DOI: 10.1101/gr.2821705
+Reference-DOI: 10.1101/gr.2821705
 Homepage: http://probcons.stanford.edu/
 Name: ProbCons
-PMID: 15687296
+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

Modified: trunk/packages/proda/trunk/debian/upstream
===================================================================
--- trunk/packages/proda/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/proda/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
-DOI: 10.1093/nar/gkl511
+Reference-DOI: 10.1093/nar/gkl511
 Name: ProDA
 Homepage: http://proda.stanford.edu/
-PMID: 17068081
+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

Modified: trunk/packages/python-pynast/trunk/debian/upstream
===================================================================
--- trunk/packages/python-pynast/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/python-pynast/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Name: PyNAST
 Homepage: http://pynast.sourceforge.net/
-DOI: 10.1093/bioinformatics/btp636
-PMID: 19914921
+Reference-DOI: 10.1093/bioinformatics/btp636
+Reference-PMID: 19914921
 Reference:
   Author: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight
   Title: PyNAST: a flexible tool for aligning sequences to a template alignment

Modified: trunk/packages/qiime/trunk/debian/upstream
===================================================================
--- trunk/packages/qiime/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/qiime/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Name: QIIME
 Homepage: http://www.qiime.org/
-DOI: 10.1038/nmeth.f.303
-PMID: 20383131
+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

Modified: trunk/packages/raster3d/trunk/debian/upstream
===================================================================
--- trunk/packages/raster3d/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/raster3d/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,6 +1,6 @@
 Homepage: http://skuld.bmsc.washington.edu/raster3d/
 Name: Raster3D
-PMID: 18488322
+Reference-PMID: 18488322
 Reference:
  Article: MerrittBacon1997
  Author: Merritt, E.A. and Bacon, D.J.

Modified: trunk/packages/raxml/trunk/debian/upstream
===================================================================
--- trunk/packages/raxml/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/raxml/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
-DOI: 10.1093/bioinformatics/btl446
+Reference-DOI: 10.1093/bioinformatics/btl446
 Homepage: http://wwwkramer.in.tum.de/exelixis/software.html
 Name: RAxML
-PMID: 16928733
+Reference-PMID: 16928733
 Reference:
   author: 16928733
   title: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Modified: trunk/packages/rnahybrid/trunk/debian/upstream
===================================================================
--- trunk/packages/rnahybrid/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/rnahybrid/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
-DOI: 10.1261/rna.5248604
+Reference-DOI: 10.1261/rna.5248604
 Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
 Name: RNAhybrid
-PMID: 15383676
+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

Modified: trunk/packages/rostlab/libzerg/trunk/debian/upstream
===================================================================
--- trunk/packages/rostlab/libzerg/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/rostlab/libzerg/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,5 +1,5 @@
 Contact: Apuã Paquola <apuapaquola at gmail.com>
-DOI: 10.1093/bioinformatics/btg122
+Reference-DOI: 10.1093/bioinformatics/btg122
 Homepage: http://code.google.com/p/libzerg/
 Name: libzerg
 Reference:

Modified: trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,5 +1,5 @@
 Contact: Apuã Paquola <apuapaquola at gmail.com>
-DOI: 10.1093/bioinformatics/btg122
+Reference-DOI: 10.1093/bioinformatics/btg122
 Homepage: http://code.google.com/p/libzerg/
 Name: libzerg-perl
 Reference:

Modified: trunk/packages/seqan/trunk/debian/upstream
===================================================================
--- trunk/packages/seqan/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/seqan/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,9 +1,9 @@
 Contact: SeqAn Team (http://www.seqan.de/contact-us.html)
-DOI: 10.1186/1471-2105-9-11
+Reference-DOI: 10.1186/1471-2105-9-11
 Donate: http://www.seqan.de/
 Homepage: http://www.seqan.de/
 Name: SeqAn
-PMID: 18184432
+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

Modified: trunk/packages/sigma-align/trunk/debian/upstream
===================================================================
--- trunk/packages/sigma-align/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/sigma-align/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Rahul Siddharthan <rsidd AT imsc.res.in>
-DOI: 10.1186/1471-2105-7-143
+Reference-DOI: 10.1186/1471-2105-7-143
 Homepage: http://www.imsc.res.in/~rsidd/sigma/
-PMID: 16542424
+Reference-PMID: 16542424
 Name: Sigma
 Reference:
  AUTHOR: Siddharthan, Rahul

Modified: trunk/packages/t-coffee/trunk/debian/upstream
===================================================================
--- trunk/packages/t-coffee/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/t-coffee/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Cédric Notredame <cedric.notredame at europe.com>
-DOI: 10.1006/jmbi.2000.4042
+Reference-DOI: 10.1006/jmbi.2000.4042
 Name: T-Coffee
 Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-PMID: 10964570
+Reference-PMID: 10964570
 Reference-Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa
 Reference-Journal: Journal of Molecular Biology
 Reference-Number: 1

Modified: trunk/packages/tm-align/trunk/debian/upstream
===================================================================
--- trunk/packages/tm-align/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/tm-align/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Yang Zhang <zhng at umich.edu>
-DOI: 10.1093/nar/gki524
+Reference-DOI: 10.1093/nar/gki524
 Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
-PMID: 15849316
+Reference-PMID: 15849316
 Name: TM-align & TM-score
 Reference:
  AUTHOR: Y. Zhang, J. Skolnick

Modified: trunk/packages/transtermhp/trunk/debian/upstream
===================================================================
--- trunk/packages/transtermhp/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/transtermhp/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,7 +1,7 @@
 Contact: Carl Kingsford <carlk at umiacs.umd.edu>
-DOI: 10.1186/gb-2007-8-2-r22
+Reference-DOI: 10.1186/gb-2007-8-2-r22
 Homepage: http://transterm.cbcb.umd.edu/
-PMID: 17313685
+Reference-PMID: 17313685
 Name: TransTermHP
 Reference:
  AUTHOR: C. Kingsford, K. Ayanbule, S.L. Salzberg

Modified: trunk/packages/velvet/trunk/debian/upstream
===================================================================
--- trunk/packages/velvet/trunk/debian/upstream	2012-02-18 01:17:47 UTC (rev 9701)
+++ trunk/packages/velvet/trunk/debian/upstream	2012-02-18 01:23:39 UTC (rev 9702)
@@ -1,8 +1,8 @@
 Contact: Daniel Zerbino <zerbino at ebi.ac.uk>
-DOI: 10.1101/gr.074492.107
+Reference-DOI: 10.1101/gr.074492.107
 Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
 Name: Velvet
-PMID: 18349386
+Reference-PMID: 18349386
 Reference:
   author: Zerbino, Daniel R. and Birney, Ewan
   title: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs


