[Blends-commit] r1774 - projects/med/trunk/debian-med/tasks

Debian Pure Blends Subversion Commit noreply at alioth.debian.org
Tue Aug 18 13:25:57 UTC 2009 

Author: tille
Date: Tue Aug 18 13:25:57 2009
New Revision: 1774
URL: http://svn.debian.org/viewsvn/blends?rev=1774&view=rev

Log:
acedb is in new with specific binary names.  WHen using these the packages are found by the blends tools
s/Depends/Recommends/


Modified:
   projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1774&view=diff&r1=1774&r2=1773&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Aug 18 13:25:57 2009
@@ -3,60 +3,60 @@
  This metapackage will install Debian packages related to molecular biology,
  structural biology and bioinformatics for use in life sciences.
 
-Depends:     altree, fastdnaml, njplot, tree-puzzle | tree-ppuzzle, treeviewx
+Recommends:     altree, fastdnaml, njplot, tree-puzzle | tree-ppuzzle, treeviewx
 Why:         Phylogenetic analysis.
 
-Depends:     molphy, phylip, treetool
+Recommends:     molphy, phylip, treetool
 Why:         Phylogenetic analysis (Non-free, thus only suggested).
 
-Depends:     fastlink, loki, plink, r-cran-qtl
+Recommends:     fastlink, loki, plink, r-cran-qtl
 Why:         Genetics
 
-Depends:     amap-align, blast2, boxshade, dialign, dialign-tx, gff2aplot, hmmer, kalign, mafft, mummer, muscle, poa, probcons, proda, seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
+Recommends:     amap-align, blast2, boxshade, dialign, dialign-tx, gff2aplot, hmmer, kalign, mafft, mummer, muscle, poa, probcons, proda, seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
 Why:         Sequence alignments and related programs.
 
-Depends:     last-align, maq, ssake, velvet
+Recommends:     last-align, maq, ssake, velvet
 Why:         Tools related to high-throughput sequencing.
 
-Depends:     emboss, embassy-domalign, embassy-domainatrix
+Recommends:     emboss, embassy-domalign, embassy-domainatrix
 Suggests:    emboss-explorer
 Why:         The EMBOSS sequence analysis suite and its galaxy.
 
-Depends:     arb, clustalw | clustalw-mpi, clustalx
+Recommends:     arb, clustalw | clustalw-mpi, clustalx
 Why:         Sequence alignments and related programs (Non-free, thus only suggested).
 
-Depends:     infernal, rnahybrid
+Recommends:     infernal, rnahybrid
 Why:         For the analysis of RNA sequences.
 
-Depends:     adun.app, garlic, gamgi, gdpc, ghemical, gromacs, pymol, rasmol, r-other-bio3d, massxpert
+Recommends:     adun.app, garlic, gamgi, gdpc, ghemical, gromacs, pymol, rasmol, r-other-bio3d, massxpert
 Why:         Molecular modelling and molecular dynamics.
 Comment:     r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team
 
-Depends:     plasmidomics
+Recommends:     plasmidomics
 Why:         Presentation
 
-Depends:     biosquid, gff2ps, mipe, melting, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, primer3, readseq, tigr-glimmer
+Recommends:     biosquid, gff2ps, mipe, melting, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, primer3, readseq, tigr-glimmer
 Why:         Tools for the molecular biologist.
 
 Suggests:    mozilla-biofox
 Why:         Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
 
-Depends:     glam2
+Recommends:     glam2
 Why:         Motif search
 
-Depends:     sequenceconverter.app
+Recommends:     sequenceconverter.app
 
-Depends: raster3d
+Recommends: raster3d
 
-Depends: phyml
+Recommends: phyml
 
-Depends: autodock
+Recommends: autodock
 Friends: autogrid
 Registration: http://autodock.scripps.edu/downloads/autodock-registration
 Why:         Molecular modelling and molecular dynamics.
 
 
-Depends: autodocktools
+Recommends: autodocktools
 Friends: mgltools-dejavu, mgltools-pmv, mgltools-utpackages, mgltools-vision, mgltools-volume, mgltools-bhtree, mgltools-geomutils, mgltools-opengltk, mgltools-pyglf, mgltools-sff
 Comment: The package autodocktools depends from the mgltools-* packages mentioned
          above, so they will be installed even if they would not be mentioned in
@@ -65,11 +65,11 @@
          http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3
          so they are mentioned here in addition to autodocktools.
 
-Depends: mustang
+Recommends: mustang
 
-Depends: theseus
+Recommends: theseus
 
-Depends: pdb2pqr
+Recommends: pdb2pqr
 Homepage: http://pdb2pqr.sourceforge.net/
 Responsible: Manuel Prinz <debian at pinguinkiste.de>
 License: GPL
@@ -88,7 +88,7 @@
  Debian already. I have had good contact with both upstream authors in
  the past.
 
-Depends: r-other-genabel
+Recommends: r-other-genabel
 Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
 Responsible: Steffen Moeller <steffen_moeller at gmx.de>
 License: GPL 2+
@@ -98,7 +98,7 @@
  A package for genome-wide association analysis between quantitative
  or binary traits and single-nucleiotide polymorphisms (SNPs).
 
-Depends: meme
+Recommends: meme
 Homepage: http://meme.nbcr.net/meme/
 Responsible: Steffen Moeller <moeller at debian.org>
 License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
@@ -117,7 +117,7 @@
  techniques to automatically choose the best width, number of occurrences,
  and description for each motif.
 
-Depends: vienna-rna
+Recommends: vienna-rna
 Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
 Responsible: Steffen Moeller <moeller at debian.org>
 License: non-free but redistributable
@@ -127,7 +127,7 @@
  stand-alone programs for the prediction and comparison of RNA secondary
  structures.
 
-Depends: cytoscape
+Recommends: cytoscape
 Homepage: http://cytoscape.org/
 Responsible: Mike Smoot <mes at aescon.com>
 License: LGPL
@@ -137,7 +137,7 @@
  interaction networks and integrating these interactions with gene expression
  profiles and other state data.  Additional features are available as plugins.
 
-Depends: ballview
+Recommends: ballview
 Homepage: http://www.ballview.org
 Responsible: Andreas Hildebrandt <anhi at bioinf.uni-sb.de>
 Pkg-URL: http://ftp-master.debian.org/new/ball_1.3+beta2.1-2.html
@@ -159,7 +159,7 @@
  for Molecular Mechanics, advanced solvation methods, comparison and
  analysis of protein structures, file import/export, and visualization.
 
-Depends: raxml
+Recommends: raxml
 Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
 License: GPL
 Pkg-Description: Randomized Axelerated Maximum Likelihood
@@ -171,7 +171,7 @@
  http://phylobench.vital-it.ch/raxml-bb/ and
  http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .
 
-Depends: axparafit
+Recommends: axparafit
 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
 Responsible: David Paleino <d.paleino at gmail.com>
 License: GPL
@@ -183,7 +183,7 @@
  for compute clusters and was used to carry out the largest
  co-evolutionary analysis to date for the paper describing the software.
 
-Depends: axpcoords
+Recommends: axpcoords
 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
 Responsible: David Paleino <d.paleino at gmail.com>
 License: GPL
@@ -196,7 +196,7 @@
  This program is required for the pipeline that conducts a full host-parasite
  co-phylogenetic analysis in combination with AxParafit.
 
-Depends: copycat
+Recommends: copycat
 Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
 License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
 Pkg-Description: fast access to cophylogenetic analyses
@@ -207,7 +207,7 @@
  creation of customized host-parasite association data and the
  computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
 
-Depends: btk-core
+Recommends: btk-core
 Homepage: http://sourceforge.net/projects/btk/
 Responsible: Morten Kjeldgaard <mok at bioxray.au.dk>
 License: GPL
@@ -218,7 +218,7 @@
  for common tasks in structural biology to facilitate the development of
  molecular modeling, design and analysis tools.
 
-Depends: tacg
+Recommends: tacg
 Homepage: http://sourceforge.net/projects/tacg
 Responsible: Charles Plessy <plessy at debian.org>
 License: GPL and others
@@ -244,7 +244,7 @@
  The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
  BMC Bioinformatics. 3:8  http://www.biomedcentral.com/1471-2105/3/8
 
-Depends: treeplot
+Recommends: treeplot
 Responsible: Charles Plessy <plessy at debian.org>
 License: GPL
 WNPP: 461508
@@ -263,7 +263,7 @@
  package.'  So this package should probably be delisted in favour of
  populations (see http://lists.debian.org/debian-med/2008/03/msg00124.html).
 
-Depends: treevolve
+Recommends: treevolve
 Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
 Responsible: Charles Plessy <plessy at debian.org>
 License: has to be verified
@@ -285,7 +285,7 @@
  Citation: Population dynamics of HIV-1 inferred from gene sequences
  Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.
 
-Depends: asap
+Recommends: asap
 Homepage: http://asap.ahabs.wisc.edu/software/asap/
 Responsible: Andreas Tille <tille at debian.org>
 License: GPL
@@ -312,7 +312,7 @@
  installations come to pass, ASAP will be further extended to be
  inter-operable between sites.
 
-Depends: emboss-kaptain
+Recommends: emboss-kaptain
 Homepage: http://userpage.fu-berlin.de/~sgmd/download.html
 Responsible: Charles Plessy <plessy at debian.org>
 License: GPL-2+
@@ -325,7 +325,7 @@
  analysis.  With EMBOSS.kaptn it integrates nicely into X window based
  desktops like KDE.
 
-Depends: agdbnet
+Recommends: agdbnet
 Homepage: http://pubmlst.org/software/database/agdbnet/
 Responsible: Andreas Tille <tille at debian.org>
 License: GPL
@@ -348,7 +348,7 @@
   * Campylobacter flaA
   * Streptococcus equi seM
 
-Depends: martj
+Recommends: martj
 Homepage: http://www.ebi.ac.uk/biomart/
 Responsible: Steffen Moeller <moeller at debian.org>
 License: GPL
@@ -359,7 +359,7 @@
  to the following data sources: UniProt Proteomes, Macromolecular
  Structure Database (MSD), Ensembl, Vega, and dbSNP.
 
-Depends: cluster3
+Recommends: cluster3
 Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
 License: non-free
 WNPP: 286167
@@ -375,7 +375,7 @@
  distance and the city-block distance were added to the available
  measures of similarity.
 
-Depends: jmol
+Recommends: jmol
 Homepage: http://jmol.sourceforge.net/
 Responsible: Vincent Fourmond <fourmond at debian.org>
 License: LGPL
@@ -398,7 +398,7 @@
  http://lists.debian.org/debian-med/2008/03/msg00097.html before
  you might download the source packages http://debian.wgdd.de/temp/jmol/
 
-Depends: jtreeview
+Recommends: jtreeview
 Homepage: http://jtreeview.sourceforge.net/
 Responsible: Steffen Moeller <moeller at debian.org>
 License: GPL
@@ -415,7 +415,7 @@
  Java TreeView is an extensible viewer for microarray data in
  PCL or CDT format.
 
-Depends: smile
+Recommends: smile
 Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
 Responsible: Steffen Moeller <moeller at debian.org>
 WNPP: 221492
@@ -430,7 +430,7 @@
  The specificity of SMILE is to allow to deal with what we call structured
  motifs, which are motifs associated by some distance constraints.
 
-Depends: cactus
+Recommends: cactus
 Homepage: http://www.cactuscode.org/Community/Biology.html
 License: GPL
 Pkg-Description:
@@ -444,7 +444,7 @@
  Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
  adaptive mesh refinement, web interfaces, and advanced visualization tools.
 
-Depends: contralign
+Recommends: contralign
 Homepage: http://contra.stanford.edu/contralign/
 License: Public Domain
 Pkg-Description: parameter learning framework for protein pairwise sequence alignment
@@ -455,7 +455,7 @@
  previously unseen sequences and avoid overfitting by controlling model
  complexity through regularization.
 
-Depends: galaxy
+Recommends: galaxy
 Homepage: http://g2.trac.bx.psu.edu/
 License: MIT
 WNPP: 432472
@@ -466,7 +466,7 @@
  strong ties with the UCSC genome browser, and makes it easy to
  visualise modified annotation files as a custom track.
 
-Depends: genographer
+Recommends: genographer
 Homepage: http://hordeum.oscs.montana.edu/genographer/
 License: GPL
 Pkg-Description: read data and reconstruct them into a gel image
@@ -478,7 +478,7 @@
  The program is written in Java and uses the Java 1.3 API. Therefore,
  it should run on any machine that can run java.
 
-Depends: molekel
+Recommends: molekel
 Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
 License: GPL
 Pkg-Description: multiplatform molecular visualization
@@ -486,7 +486,7 @@
  program being developed at the Swiss National Supercomputing Centre
  (CSCS).
 
-Depends: pftools
+Recommends: pftools
 Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
 License: GPL
 Pkg-Description: tools to handle patterns from PROSITE
@@ -495,7 +495,7 @@
  in Swiss-Prot or FASTA format. It requires two compiled external
  programs from the PFTOOLS, which are also distributed with the sources.
 
-Depends: proalign
+Recommends: proalign
 Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
 License: GPL
 Responsible: Charles Plessy <plessy at debian.org>
@@ -515,7 +515,7 @@
  characters according to an evolutionary model. It has been published in
  Bioinformatics. 2003 Aug 12;19(12):1505-13.
 
-Depends: ssaha
+Recommends: ssaha
 Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
 License: GPL
 Responsible: Charles Plessy <plessy at debian.org>
@@ -535,7 +535,7 @@
  http://www.sanger.ac.uk/Software/analysis/SSAHA2/
  does not seem to be available.
 
-Depends: ngila
+Recommends: ngila
 Homepage: http://scit.us/projects/ngila/
 License: GPLv3
 Responsible: Charles Plessy <plessy at debian.org>
@@ -560,7 +560,7 @@
  Ngila is published in Cartwright RA Bioinformatics 2007
  23(11):1427-1428; doi:10.1093/bioinformatics/btm095
 
-Depends: tm-align
+Recommends: tm-align
 Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
 License: free to change and redistribute
 Responsible: Steffen Moeller <moeller at debian.org>
@@ -574,7 +574,7 @@
  TM-align performs a structural alignment of protein sequences. It is
  said to be 10 times faster than DALI and no worse in accuracy.
 
-Depends: staden-io-lib-utils
+Recommends: staden-io-lib-utils
 Homepage: http://staden.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/staden-io-lib/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/staden-io-lib/trunk/
@@ -592,7 +592,7 @@
  to maniuplate short reads generated by second and third generation sequencers
  and stored in SRF format.
 
-Depends: dazzle
+Recommends: dazzle
 Homepage: http://www.biojava.org/dazzle
 Responsible: Steffen Moeller <moeller at debian.org>
 License: LGPL
@@ -607,7 +607,7 @@
  .
  Information on DAS is available from http://www.biodas.org/
 
-Depends: ecell
+Recommends: ecell
 Homepage: http://www.e-cell.org/
 Responsible: Steffen Moeller <moeller at debian.org>
 WNPP: 241195
@@ -632,7 +632,7 @@
   * E-Cell Modeling Environment (or E-Cell ME)
   * E-Cell Analysis Toolkit.
 
-Depends: ncoils
+Recommends: ncoils
 Homepage: http://www.russell.embl.de/cgi-bin/coils-svr.pl
 Responsible: Steffen Moeller <moeller at debian.org>
 WNPP: 299856
@@ -644,7 +644,7 @@
  Lupas, van Dyke & Stock, Predicting coiled coils from
  protein sequences Science, 252, 1162-1164, 1991.
 
-Depends: haploview
+Recommends: haploview
 Homepage: http://www.broad.mit.edu/mpg/haploview/
 Responsible: Steffen Moeller <moeller at debian.org>
 WNPP: 311421
@@ -656,7 +656,7 @@
  to determine genes and genetic pathways that are associated
  with diseases. This is an early stage in the quest for new drugs.
 
-Depends: bio-mauve
+Recommends: bio-mauve
 Homepage: http://asap.ahabs.wisc.edu/mauve/
 Responsible: Andreas Tille <tille at debian.org>
 License: GPL
@@ -685,7 +685,7 @@
  Note: There are instructions for compiling Mauve from source available at
  http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html
 
-Depends: mauvealigner
+Recommends: mauvealigner
 Homepage: http://asap.ahabs.wisc.edu/mauve/
 Responsible: Andreas Tille <tille at debian.org>
 License: GPL
@@ -718,7 +718,7 @@
  .
  Mauve is developed at the University of Wisconsin.
 
-Depends: gbrowse
+Recommends: gbrowse
 Homepage: http://www.gmod.org/wiki/index.php/GBrowse
 Responsible: Charles Plessy <plessy at debian.org>
 WNPP: 429610
@@ -742,7 +742,7 @@
   * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
     find oligonucleotides, design primers, create restriction maps, edit features)
 
-Depends: mira
+Recommends: mira
 Homepage: http://chevreux.org/projects_mira.html
 Responsible: Charles Plessy <plessy at debian.org>
 WNPP: 435915
@@ -761,7 +761,7 @@
  between organisms, and pristine assembly of sequences from various
  sources for oligo design in clinical microarray experiments.
 
-Depends: phylographer
+Recommends: phylographer
 Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
 Responsible: Charles Plessy <plessy at debian.org>
 WNPP: 426489
@@ -780,7 +780,7 @@
  biological sequence alignment reports (BLAST is provided by Debian's
  blast2 package).
 
-Depends: phylowin
+Recommends: phylowin
 Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
 Responsible: Charles Plessy <plessy at debian.org>
 WNPP: 395840
@@ -799,7 +799,7 @@
  its use for profit.  Therfore, Phylo_win will unfortunately have to be
  distributed in contrib or non-free.
 
-Depends: seq-gen
+Recommends: seq-gen
 Homepage: http://tree.bio.ed.ac.uk/software/seqgen/
 License: Free
 Pkg-Description: simulate the evolution of nucleotide or amino acid sequences
@@ -815,7 +815,7 @@
  incorporates most of the commonly used (and computationally tractable)
  models of molecular sequence evolution.
 
-Depends: wgs-assembler
+Recommends: wgs-assembler
 Homepage: http://wgs-assembler.sourceforge.net/
 Responsible: Charles Plessy <plessy at debian.org>
 WNPP: 395843
@@ -859,7 +859,7 @@
  See also: http://www.jcvi.org/cms/research/software/celera-assembler/overview/
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: gbioseq
+Recommends: gbioseq
 Homepage: http://www.bioinformatics.org/project/?group_id=94
 License: GPL
 Pkg-Description: DNA sequence editor for Linux
@@ -867,7 +867,7 @@
  The goal is to provide an easy to use software to edit DNA sequences under
  Linux, Windows, MacOsX, using GTK C# (Mono).
 
-Depends: populations
+Recommends: populations
 Homepage: http://bioinformatics.org/~tryphon/populations/
 License: GPL
 Pkg-Description: individuals or populations distances based on allelic frequencies
@@ -884,14 +884,14 @@
   * Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
     Populations...)
 
-Depends: phpphylotree
+Recommends: phpphylotree
 Homepage: http://www.bioinformatics.org/project/?group_id=372
 License: GPL
 Pkg-Description: draw phylogenetic trees
  PhpPhylotree is a web application that is able to draw phylogenetic trees.
  It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
 
-Depends: tracetuner
+Recommends: tracetuner
 Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview
 License: GPL; but US Patent #6,681,186
 Pkg-Description: DNA sequencing and trace processing
@@ -920,7 +920,7 @@
  and conditions of the GNU General Public License, version 2, as published by the
  Free Software Foundation (the "GNU General Public License").
 
-Depends: twain
+Recommends: twain
 Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml
 License: Open Source
 Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model
@@ -943,7 +943,7 @@
  Slides from a talk at Computational Genomics 2004 are now available.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: rose
+Recommends: rose
 Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
 License: Open Source
 Pkg-Description: Region-Of-Synteny Extractor
@@ -962,7 +962,7 @@
  boundaries of the output region.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: glimmerhmm
+Recommends: glimmerhmm
 Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
 License: Artistic
 Pkg-Description: Eukaryotic Gene-Finding System
@@ -977,7 +977,7 @@
  user manual can be consulted here.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: genezilla
+Recommends: genezilla
 Homepage: http://www.genezilla.org/
 License: Artistic
 Pkg-Description: eukaryotic gene finder
@@ -1004,7 +1004,7 @@
  for the comparative gene finder TWAIN.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: exalt
+Recommends: exalt
 Homepage: http://www.cbcb.umd.edu/software/exalt/
 License: Artistic
 Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
@@ -1018,7 +1018,7 @@
  run on other species.
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: jigsaw
+Recommends: jigsaw
 Homepage: http://www.cbcb.umd.edu/software/jigsaw/
 License: Artistic
 Pkg-Description: gene prediction using multiple sources of evidence
@@ -1046,7 +1046,7 @@
  custom tracks in the UCSC Human Genome Browser
 Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)
 
-Depends: genesplicer
+Recommends: genesplicer
 Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
 License: Artistic
 Pkg-Description: computational method for splice site prediction
@@ -1113,7 +1113,7 @@
  packaging effort is stalled.  Feel free to tell us, if you are
  interested in turning this into an official package.
 
-Depends: mummergpu
+Recommends: mummergpu
 Homepage: http://mummergpu.sourceforge.net/
 License: Artistic
 Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
@@ -1141,7 +1141,7 @@
  technologies.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: amos-assembler
+Recommends: amos-assembler
 Homepage: http://amos.sourceforge.net/
 License: Artistic
 Pkg-Description: modular whole genome assembler
@@ -1158,7 +1158,7 @@
  design philosophy and a software system.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: amoscmp
+Recommends: amoscmp
 Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
 License: Artistic
 Pkg-Description: comparative genome assembly package
@@ -1187,7 +1187,7 @@
  modular open-source framework for assembly development.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: minimus
+Recommends: minimus
 Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
 License: Artistic
 Pkg-Description: AMOS lightweight assembler
@@ -1279,7 +1279,7 @@
 Note: Found at
  http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337
 
-Depends: mage2tab
+Recommends: mage2tab
 Homepage: https://www.cbil.upenn.edu/magewiki/index.php/mage2tab
 License: CBIL Software and Data License (Apache-like)
 WNPP: 476209
@@ -1291,7 +1291,7 @@
  MINiML) from or into databases like GUS (the Genomics Unified Schema,
  www.gusdb.org).
 
-Depends: bambus
+Recommends: bambus
 Homepage: http://amos.sourceforge.net/docs/bambus/
 License: Artistic
 Pkg-Description: hierarchical approach to building contig scaffolds
@@ -1306,7 +1306,7 @@
  integrated with the AMOS package (see http://amos.sourceforge.net/)
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: hawkeye
+Recommends: hawkeye
 Homepage: http://amos.sourceforge.net/hawkeye/
 License: Artistic
 Pkg-Description: Interactive Visual Analytics Tool for Genome Assemblies
@@ -1339,7 +1339,7 @@
  assemblies. Genome Biology 8:R34.
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
-Depends: murasaki
+Recommends: murasaki
 Homepage: http://murasaki.dna.bio.keio.ac.jp/
 License: GPL
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/murasaki/trunk/
@@ -1358,7 +1358,7 @@
   * repeat tolerant
   * intelligent noise reduction
 
-Depends: gmv
+Recommends: gmv
 Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
 License: GPL
 Pkg-Description: comparative genome browser for Murasaki
@@ -1366,14 +1366,14 @@
  anchors from Murasaki, annotation data from GenBank files, and
  expression / prediction score from GFF files.
 
-Depends: pyrophosphate-tools
+Recommends: pyrophosphate-tools
 Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html
 License: not specified
 Pkg-Description: for assembling and searching pyrophosphate sequence data
  Simple tools for assembling and searching high-density picolitre
  pyrophosphate sequence data.
 
-Depends: figaro
+Recommends: figaro
 Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
 License: Artistic
 Pkg-Description: novel vector trimming software
@@ -1387,7 +1387,7 @@
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
 
 
-Depends: mirbase
+Recommends: mirbase
 Homepage: http://microrna.sanger.ac.uk/
 License: Public Domain
 WNPP: 420938
@@ -1410,7 +1410,7 @@
  It is possible that mirbase will not be a package from the main archive, but
  will be autogenerated as part of a larger data packaging effort.
 
-Depends: elph
+Recommends: elph
 Homepage: http://www.cbcb.umd.edu/software/ELPH/
 License: Artistic
 Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites
@@ -1428,7 +1428,7 @@
  http://www.cbcb.umd.edu/software/SeeEse/index.html .
 Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
 
-Depends: repeatfinder
+Recommends: repeatfinder
 Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
 License: Artistic
 Pkg-Description: finding repetitive sequences complete and draft genomes
@@ -1442,7 +1442,7 @@
  Kurtz's REPuter.
 Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
 
-Depends: reputer
+Recommends: reputer
 Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
 License: to be clarified
 Pkg-Description: fast computation of maximal repeats in complete genomes
@@ -1450,7 +1450,7 @@
  palindromes in entire genomes very efficiently.
 Note: Download site (temporarily) not available - try to contact author
 
-Depends: transtermhp
+Recommends: transtermhp
 Homepage: http://transterm.cbcb.umd.edu/index.php
 License: Free
 Pkg-Description: finds rho-independent transcription terminators in bacterial genomes
@@ -1463,7 +1463,7 @@
  relationship to DNA uptake. Genome Biology 8:R22 (2007).
 Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)
 
-Depends: patman
+Recommends: patman
 Homepage: http://bioinf.eva.mpg.de/patman/
 License: GPL-2+
 WNPP: 482555
@@ -1473,7 +1473,7 @@
  for approximate matches. It is optimized for searching for many small
  pattern at the same time, for example microarray probes.
 
-Depends: uniprime
+Recommends: uniprime
 Homepage: http://code.google.com/p/uniprime/
 License: GPL-3+
 Responsible: Charles Plessy <plessy at debian.org>
@@ -1489,7 +1489,7 @@
  generates successful cross-species primers that take into account the
  biological aspects of the PCR.
 
-Depends: genetrack
+Recommends: genetrack
 Homepage: http://sysbio.bx.psu.edu/genetrack.html
 License: MIT
 Responsible: Charles Plessy <plessy at debian.org>
@@ -1499,7 +1499,7 @@
  analyze data obtained via high-throughput rapid sequencing platforms such as
  the 454 and Solexa as well as tiling array data based on various platforms.
 
-Depends: operondb
+Recommends: operondb
 Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
 License: to be clarified
 Pkg-Description: detect and analyze conserved gene pairs
@@ -1528,7 +1528,7 @@
  no info about license or downloadable code found, but tried to
  contact authors.
 
-Depends: trnascan-se
+Recommends: trnascan-se
 Homepage: http://lowelab.ucsc.edu/tRNAscan-SE/
 License: GPL
 Pkg-Description: program for improved detection of transfer RNA genes in genomic sequence
@@ -1544,7 +1544,7 @@
  homologues such as selenocysteine tRNAs, tRNA-derived repetitive
  elements and tRNA pseudogenes.
 
-Depends: beast-mcmc
+Recommends: beast-mcmc
 Homepage: http://beast.bio.ed.ac.uk/
 License: LGPL
 Pkg-Description: Bayesian MCMC analysis of molecular sequences
@@ -1564,7 +1564,7 @@
  There is a Debian package beast which is completely unrelated
  to this project.
 
-Depends: artemis
+Recommends: artemis
 Homepage: http://www.sanger.ac.uk/Software/Artemis/
 License: GPL 2+
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -1579,7 +1579,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: srf
+Recommends: srf
 Homepage: http://srf.sourceforge.net/
 License: Apache License V2.0
 WNPP: 489983
@@ -1600,7 +1600,7 @@
  This splits up into a library package which reads the format and a
  doc package which documents to format.
 
-Depends: alien-hunter
+Recommends: alien-hunter
 Homepage: http://www.sanger.ac.uk/Software/analysis/alien_hunter/
 License: GPL
 Pkg-Description: Interpolated Variable Order Motifs for identification of horizontally acquired DNA
@@ -1627,7 +1627,7 @@
  So stripping the copy of BioJava from the source package
  seem to be a good idea.
 
-Depends: act
+Recommends: act
 Homepage: http://www.sanger.ac.uk/Software/ACT/
 License: GPL
 Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
@@ -1649,7 +1649,9 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: acedb
+Recommends: acedb-other-dotter, acedb-other-belvu
+
+Recommends: acedb-other
 Homepage: http://www.acedb.org/
 License: GPL / LGPL
 Language: C, C++
@@ -1685,7 +1687,7 @@
  this is probably also not for us except somebody has real interest
  and volunteers to clarify the license.
 
-Depends: cdna-db
+Recommends: cdna-db
 Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
 License: Artistic
 Pkg-Description: quality-control checking of finished cDNA clone sequences
@@ -1712,7 +1714,7 @@
  dump cDNA clones sequences (such as those that passed the QC
  checking) from the cdna_db.
 
-Depends: das-proserver
+Recommends: das-proserver
 Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
 License: Same as Perl
 Pkg-Description: lightweight Distributed Annotation System (DAS) server
@@ -1749,7 +1751,7 @@
  last years we have also seen growing acceptance in the protein
  sequence and structure communities.
 
-Depends: spice
+Recommends: spice
 Homepage: http://www.efamily.org.uk/software/dasclients/spice/
 License: GPL
 Pkg-Description: Distributed Annotation System (DAS) client
@@ -1763,7 +1765,7 @@
  possible to add new annotations to SPICE, and to compare them with
  the already available information.
 
-Depends: decipher
+Recommends: decipher
 Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
 License: To be clarified
 Pkg-Description: tracks duplications and deletions of DNA in patients
@@ -1775,7 +1777,7 @@
  of these conditions. DECIPHER makes use of DAS technology to
  integrate with Ensembl, the world's leading genome browser.
 
-Depends: est-db
+Recommends: est-db
 Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
 License: Artistic
 Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
@@ -1806,7 +1808,7 @@
  available free of charge, and, where possible, similarly
  open-licensed components have been used in its development.
 
-Depends: finex
+Recommends: finex
 Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
 License: To be clarified
 Pkg-Description: sequence homology searching
@@ -1817,7 +1819,7 @@
  Please note FINEX is no longer supported but is available for
  download.
 
-Depends: hexamer
+Recommends: hexamer
 Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
 License: GPL
 Pkg-Description: scan DNA sequences to look for likely coding regions
@@ -1844,7 +1846,7 @@
     converted to 'c'.
     The output of hexamer is in General Feature Format (GFF) format.
 
-Depends: logomat-m
+Recommends: logomat-m
 Homepage: http://www.sanger.ac.uk/Software/analysis/logomat-m/
 License: As Perl itself
 Pkg-Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
@@ -1865,7 +1867,7 @@
  Rahmann S BMC Bioinformatics. 2004;5;7. PMID: 14736340 DOI:
  10.1186/1471-2105-5-7
 
-Depends: coot
+Recommends: coot
 Homepage: http://www.ysbl.york.ac.uk/~emsley/coot/
 License: GPL
 Pkg-Description: protein structure model-building, -completion, -validation
@@ -1874,7 +1876,7 @@
  refinement, manual rotation/translation, rigid-body fitting, ligand
  search, solvation, mutations, rotamers, Ramachandran plots...
 
-Depends: r-ape
+Recommends: r-ape
 Homepage: http://ape.mpl.ird.fr/
 License: GPL
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -1887,7 +1889,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: caftools
+Recommends: caftools
 Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
 License: Free for non-commercial purposes
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -1911,7 +1913,7 @@
  Format) or GAP4. This package includes tools to convert assemblies
  from Newbler's ace format for loading into a gap4 assembly.
 
-Depends: roche454ace2caf
+Recommends: roche454ace2caf
 Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
 License: not specified
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -1938,7 +1940,7 @@
  Format) or GAP4. This package includes tools to convert assemblies
  from Newbler's ace format for loading into a gap4 assembly.
 
-Depends: big-blast
+Recommends: big-blast
 Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl
 License: not specified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -1950,7 +1952,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: blixem
+Recommends: blixem
 Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html
 License: not specified
 Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -1963,7 +1965,7 @@
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: cap3
+Recommends: cap3
 Homepage: http://genome.cs.mtu.edu/cap/cap3.html
 License: free for governmental agency or a non-profit educational institution
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -1987,7 +1989,7 @@
  convenience to Bio-Linux users so that the files are placed in
  locations consistent with the Bio-Linux setup.
 
-Depends: cd-hit
+Recommends: cd-hit
 Homepage: http://www.bioinformatics.org/cd-hit/
 License: to be clarified
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2021,7 +2023,7 @@
  at http://www.clcbio.com/index.php?id=28 but this seems to be only
  "free as in beer" binary download - so this is not for us ...
 
-Depends: coalesce
+Recommends: coalesce
 Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
 License: not specified
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2046,7 +2048,7 @@
  at http://www.dendroscope.org but this project has only a
  "free as in beer" binary download - so this is not for us ...
 
-Depends: dotter
+Recommends: dotter
 Homepage: http://www.cgb.ki.se/cgb/groups/sonnhammer/Dotter.html
 License: to be clarified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2077,7 +2079,7 @@
  Homepage is currently unavailable but the source might be
  obtainable from freebsd.org.
 
-Depends: dotur
+Recommends: dotur
 Homepage: http://schloss.micro.umass.edu/software/dotur.html
 License: GPL
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2094,7 +2096,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: estferret
+Recommends: estferret
 Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
 License: to be clarified
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2142,7 +2144,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: estscan
+Recommends: estscan
 Homepage: http://estscan.sourceforge.net/
 License: free
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2176,7 +2178,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: fasta
+Recommends: fasta
 Homepage: http://www.ebi.ac.uk/Tools/fasta/
 License: no inclusion into commercial product
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2198,7 +2200,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: fluctuate
+Recommends: fluctuate
 Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
 License: not specified
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2219,7 +2221,7 @@
  BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
  a package.
 
-Depends: forester
+Recommends: forester
 Homepage: http://sourceforge.net/projects/forester-atv/
 License: LGPL
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2232,7 +2234,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: r-happy
+Recommends: r-happy
 Homepage: http://www.well.ox.ac.uk/happy/
 License: GPL
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2276,7 +2278,7 @@
  version available at http://www.well.ox.ac.uk/happy/happyR.shtml
  which is entirely free.
 
-Depends: jalview
+Recommends: jalview
 Homepage: http://www.jalview.org/
 License: GPL
 WNPP: 507436
@@ -2288,7 +2290,7 @@
  the Pfam protein domain database) but is available as a general
  purpose alignment editor.
 
-Depends: lamarc
+Recommends: lamarc
 Homepage: http://evolution.gs.washington.edu/lamarc/
 License: Apache V2.0
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2306,7 +2308,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: lucy
+Recommends: lucy
 Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
 License: GPL
 Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2333,7 +2335,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: maxd
+Recommends: maxd
 Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
 License: Artistic
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2352,7 +2354,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: mesquite
+Recommends: mesquite
 Homepage: http://mesquiteproject.org/mesquite/mesquite.html
 License: LGPL
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2380,7 +2382,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: migrate
+Recommends: migrate
 Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
 License: to be clarified
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2403,7 +2405,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: mrbayes
+Recommends: mrbayes
 Homepage: http://mrbayes.csit.fsu.edu/
 License: GPL
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2426,7 +2428,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: msatfinder
+Recommends: msatfinder
 Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
 License: GPL
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2442,7 +2444,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: mview
+Recommends: mview
 Homepage: http://bio-mview.sourceforge.net/
 License: GPL
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2459,7 +2461,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: oligoarrayaux
+Recommends: oligoarrayaux
 Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
 License: non-free (fre academical use)
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2486,7 +2488,7 @@
  this and so it might make soem sense to list it here - further
  investigation is needed.
 
-Depends: omegamap
+Recommends: omegamap
 Homepage: http://www.danielwilson.me.uk/software.html
 License: to be clarified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2507,7 +2509,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: paml
+Recommends: paml
 Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
 License: not specified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2524,7 +2526,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: partigene
+Recommends: partigene
 Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
 License: GPL
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2539,7 +2541,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: pfaat
+Recommends: pfaat
 Homepage: http://pfaat.sourceforge.net/
 License: GPL
 Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2552,7 +2554,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: pftools
+Recommends: pftools
 Homepage: http://www.isrec.isb-sib.ch/profile/profile.html
 License: not specified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2564,7 +2566,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: prank
+Recommends: prank
 Homepage: http://www.ebi.ac.uk/goldman-srv/prank/
 License: GPL (except two algorithms)
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2605,7 +2607,7 @@
  project has only a "free as in beer" binary download - so this is not
  for us ...
 
-Depends: prot4est
+Recommends: prot4est
 Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
 License: GPL
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2618,7 +2620,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: qtlcart
+Recommends: qtlcart
 Homepage: http://statgen.ncsu.edu/qtlcart/
 License: GPL
 Responsible: BioLinux - Dan Swan <dswan at ceh.ac.uk>
@@ -2632,7 +2634,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: rbs-finder
+Recommends: rbs-finder
 Homepage: http://www.genomics.jhu.edu/RBSfinder/
 License: not specified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2650,7 +2652,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: recombine
+Recommends: recombine
 Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
 License: not specified
 Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
@@ -2672,7 +2674,7 @@
  BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
  a package.
 
-Depends: splitstree
+Recommends: splitstree
 Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
 License: to be clarified
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2705,7 +2707,7 @@
  http://envgen.nox.ac.uk/biolinux.html
 
 
-Depends: taverna
+Recommends: taverna
 Homepage: http://taverna.sourceforge.net/
 License: LGPL
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2731,7 +2733,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: taxinspector
+Recommends: taxinspector
 Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
 License: Artistic + other free licenses
 Responsible: BioLinux - Tim Booth <tbooth at ceh.ac.uk>
@@ -2743,7 +2745,7 @@
 Remark: This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: tetra
+Recommends: tetra
 Homepage: http://www.megx.net/tetra/
 License: free academic
 Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
@@ -2763,7 +2765,7 @@
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: trace2dbest
+Recommends: trace2dbest
 Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
 License: GPL
 Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
@@ -2788,7 +2790,7 @@
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
 
-Depends: profit
+Recommends: profit
 Homepage: http://www.bioinf.org.uk/software/profit/
 License: non-free
 Responsible: Steffen Moeller <steffen_moeller at gmx.de>
@@ -2801,7 +2803,7 @@
 Remark: The authors need to change the license, still.
  The debian folder should appear in Debian Med Svn in some near future.
 
-Depends: kempbasu
+Recommends: kempbasu
 Homepage: http://code.google.com/p/kempbasu/
 License: GPL
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/kempbasu/trunk/
@@ -2816,7 +2818,7 @@
  They provide two programs: kemp for the frequentist test and basu for
  the Bayesian test, and some auxiliary scripts.
 
-Depends: samtools
+Recommends: samtools
 Homepage: http://samtools.sourceforge.net
 License: MIT
 WNPP: 540453
@@ -2829,7 +2831,7 @@
  sorting, merging and indexing, and allows to retrieve reads in any regions
  swiftly.
 
-Depends: fastx-toolkit
+Recommends: fastx-toolkit
 Homepage: http://hannonlab.cshl.edu/fastx_toolkit
 License: AGPL / MIT
 Responsible: Assaf Gordon <gordon at cshl.edu>
@@ -2849,7 +2851,7 @@
  .
  http://hannonlab.cshl.edu/crosstab/
 
-Depends: grogui
+Recommends: grogui
 Homepage: http://www.kde-apps.org/content/show.php?content=47665
 License: GPL
 Pkg-Description: graphical user interface for popular molecular dynamics package GROMACS
@@ -2862,7 +2864,7 @@
   7. MDP Writer section to easily create your mdp files.
   8. File icons based on their types.
 
-Depends: rosetta
+Recommends: rosetta
 Homepage: http://www.rosettacommons.org/
 License: not redistributable, not unlikely to change
 Pkg-Description: Protein-folding, -docking, ..?
@@ -2875,7 +2877,7 @@
  the source or binaries. Nevertheless, Debian-Med could possibly offer
  an easy preparation of Debian packages.
 
-Depends: Obo-Edit
+Recommends: obo-edit
 Homepage: http://www.geneontology.org
 License: something free
 Pkg-Description: editor for biological ontologies

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