Task: Biology
Description: Debian-Med micro-biology packages
 This meta package will install Debian packages related to molecular biology,
 structural biology and bioinformatics for use in life sciences.  Please note
 that there also recommended and only suggested packages which are not
 installed in any circumstance but only if the user asks for installing these.


Depends:     fastdnaml, njplot, tree-puzzle | tree-ppuzzle, treeviewx
Why:         Phylogenetic analysis.
Depends:     molphy, phylip, treetool
Why:         Phylogenetic analysis (Non-free, thus only suggested).

Depends:     fastlink, loki, r-cran-qtl
Why:         Genetics.

Depends:     amap-align, blast2, boxshade, dialign, gff2aplot, emboss, hmmer, kalign, mummer, muscle, poa, probcons, proda, \
             seaview, sim4, sibsim4, sigma-align, t-coffee, wise
Why:         Sequence alignments and related programs.
Depends:     arb, clustalw | clustalw-mpi, clustalx
Why          Sequence alignments and related programs (Non-free, thus only suggested).

Depends:     adun.app, garlic, gdpc, ghemical, gromacs, pymol, rasmol
Why:         Molecular modelling and molecular modelling.

Depends:     plasmidomics
Why:         Presentation

Recommends:  textopo
Why:         This is only recommended to not necessarily flood the system with TeX packages - perhaps target for -doc?

Depends:     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.

Suggests:    bugsx 
Why:         Other packages (Non-free, thus only suggested).

Depends: dialign-t
Homepage: http://dialign-t.gobics.de/
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
License: LGPL
WNPP: 445983
Pkg-Description: Segment-based multiple sequence alignment
 DIALIGN-T is a command line tool to perform multiple alignment of protein or
 DNA sequences. It is a complete reimplementation of the segment-base approach
 including several new improvements and heuristics that significantly enhance
 the quality of the output alignments compared to DIALIGN 2.2. For pairwise
 alignment, DIALIGN-T uses a fragment-chaining algorithm that favours chains of
 low-scoring local alignments over isolated high-scoring fragments. For
 multiple alignment, DIALIGN-T uses an improved greedy procedure that is less
 sensitive to spurious local sequence similarities.  DIALIGN-T has been
 published in Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
 Burkhard Morgenstern: DIALIGN-T: An improved algorithm for segment-based
 multiple sequence alignment. BMC Bioinformatics 2005, 6:66.
 .
 DIALIGN-T is needed by dm_coffee, a special mode of t_coffee prepared
 especially for Debian, in which non-free alignment software was replaced by
 free alternatives.

Depends: tm-align
Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
License: free to change and redistribute
WNPP: 447505
Pkg-Description: structural protein alignment
 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: meme
Homepage: http://meme.nbcr.net/meme/
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
Pkg-Description: motif discovery and search
  MEME is a tool for discovering motifs in a group of related DNA or protein
  sequences.  A motif is a sequence pattern that occurs repeatedly in a group
  of related protein or DNA sequences. MEME represents motifs as position-dependent
  letter-probability matrices which describe the probability of each possible
  letter at each position in the pattern. Individual MEME motifs do not contain
  gaps. Patterns with variable-length gaps are split by MEME into two or more
  separate motifs.
  .
  MEME takes as input a group of DNA or protein sequences (the training set)
  and outputs as many motifs as requested. MEME uses statistical modeling
  techniques to automatically choose the best width, number of occurrences,
  and description for each motif.

Depends: vienna-rna
Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
Responsible: Steffen Moeller <steffen_moeller@gmx.de>
License: non-free but redistributable
WNPP: 451193
Pkg-Description: RNA sequence analysis
 The Vienna RNA Package consists of a C code library and several
 stand-alone programs for the prediction and comparison of RNA secondary
 structures.

Depends: cytoscape
Homepage: http://cytoscape.org/
Responsible: Mike Smoot <mes@aescon.com>
Pkg-Description: visualizing molecular interaction networks
 Cytoscape is a bioinformatics software platform for visualizing molecular
 interaction networks and integrating these interactions with gene expression
 profiles and other state data.  Additional features are available as plugins.
 