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.

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

Suggests:    texlive-science
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.

Depends: dialign-t

Depends: glam2, exonerate

Depends: autodock, autogrid
Why: This is just in SVN and hopefully an upload will happen soon.

Suggests: biococoa.app
Why: Only suggests, because current version in Debian breaks, has new upstream -
     at least version 1.7 might run under Linux, the new designed 2.0 seems to
     work under Mac OSX only and it is not really maintained (Debian QA group).
     We want to keep track of it anyway.

Depends: meme
Homepage: http://meme.nbcr.net/meme/
Responsible: 
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)
WNPP: 
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 <moeller@debian.org>
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>
License: 
WNPP: 
Pkg-Description: visualizing molecular interaction networks
 Cytoscape is a bioinformatics software platform for visualizing molecular
 interaction networks and integrating these interactions with gene expression
 profiles and other state data.  Additional features are available as plugins.

Depends: ballview
Homepage: http://www.ballview.org
Pkg-URL: http://mentors.debian.net/debian/pool/main/b/ballview/
License: LGPL
Pkg-Description: free molecular modeling and molecular graphics tool
 BALLView provides fast OpenGL-based visualization of molecular structures,
 molecular mechanics methods (minimization, MD simulation using the
 AMBER, CHARMM, and MMFF94 force fields), calculation and visualization
 of electrostatic properties (FDPB) and molecular editing features.
 .
 BALLView is based on BALL (Biochemical Algorithms Library) ,
 which is currently being developed in the groups of Hans-Peter Lenhof
 (Saarland University, Saarbruecken, Germany) and Oliver Kohlbacher
 (University of Tuebingen, Germany). BALL is an application framework
 in C++ that has been specifically designed for rapid software
 development in Molecular Modeling and Computational Molecular Biology.
 It provides an extensive set of data structures as well as classes
 for Molecular Mechanics, advanced solvation methods, comparison and
 analysis of protein structures, file import/export, and visualization.

Depends: raxml
Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
Responsible: 
License: GPL
WNPP: 
Pkg-Description: Randomized Axelerated Maximum Likelihood
 RAxML is a program for sequential and parallel Maximum Likelihood-based
 inference of large phylogenetic trees. It has originally been derived
 from fastDNAml.
 .
 There are freely accessible web-servers available for RAxML at
 http://phylobench.vital-it.ch/raxml-bb/ and
 http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .

Depends: axparafit
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
Responsible: David Paleino <d.paleino@gmail.com>
License: GPL
WNPP: 464323
Pkg-Description: optimized statistical analysis of host-parasite coevolution
 AxParafit is a highly optimized version of Pierre Legendre's Parafit
 program for statistical analysis of host-parasite coevolution.
 AxParafit has been parallelized with MPI (Message Passing Interface)
 for compute clusters and was used to carry out the largest
 co-evolutionary analysis to date for the paper describing the software.

Depends: axpcoords
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
Responsible: 
License: GPL
WNPP: 464323
Pkg-Description: LAPACK-based implementation of DistPCoA
 AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see 
 http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
 which is another program by Pierre Legendre, it conducts a principal 
 coordinates analysis.
 This program is required for the pipeline that conducts a full host-parasite 
 co-phylogenetic analysis in combination with AxParafit.

Depends: copycat
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
Responsible: 
License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
WNPP: 
Pkg-Description: fast access to cophylogenetic analyses
 CopyCat provides an easy and fast access to cophylogenetic analyses.
 It incorporates a wrapper for the program ParaFit, which conducts a
 statistical test for the presence of congruence between host and
 parasite phylogenies. CopyCat offers various features, such as the
 creation of customized host-parasite association data and the
 computation of phylogenetic host/parasite trees based on the NCBI taxonomy.

Depends: mustang
Homepage: http://www.cs.mu.oz.au/~arun/mustang/
Responsible: Morten Kjeldgaard <mok@bioxray.au.dk>
License: 3 clause BSD
WNPP: 459637
Pkg-Description: multiple structural alignment of proteins
 Mustang is an algorithm for structural alignment of multiple
 protein structures. Given a set of PDB files, the program uses the
 spatial information in the Calpha atoms of the set to produce a sequence
 alignment. Based on a progressive pairwise heuristic the algorithm
 then proceeds through a number of refinement passes. Mustang
 reports the multiple sequence alignment and the corresponding
 superposition of structures.

Depends: btk-core
Homepage: http://sourceforge.net/projects/btk/
Responsible: Morten Kjeldgaard <mok@bioxray.au.dk>
License: GPL
WNPP: 459753
Pkg-Description: biomolecule Toolkit C++ library
 The Biomolecule Toolkit is a library for modeling biological
 macromolecules such as proteins, DNA and RNA. It provides a C++ interface
 for common tasks in structural biology to facilitate the development of
 molecular modeling, design and analysis tools.

Depends: tacg
Homepage: http://sourceforge.net/projects/tacg
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
License: GPL and others
WNPP: 461504
Pkg-Description: command line program for finding patterns in nucleic acids
 tacg is a character-based, command line tool for unix-like operating systems
 for pattern-matching in nucleic acids and performing some of the basic protein
 manipulations. It was originally designed for restriction enzyme analysis of
 DNA, but has been extended to other types of matching. It now handles
 degenerate sequence input in a variety of matching approaches, as well as
 patterns with errors, regular expressions and TRANSFAC-formatted matrices.
 .
 It was designed to be a grep for DNA and like the original grep, its
 capabilities have grown so that now the author has to keep calling up the help
 page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
 application in any sense. However, it's existance as a strictly command-line
 tool lends itself well to Webification and wrapping by various GUI tools and
 it is now distributed with a web interface form and a Perl CGI handler.
 Additionally, it can easily be integrated into editors that support shell
 commands such as nedit.
 .
 The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
 BMC Bioinformatics. 3:8  http://www.biomedcentral.com/1471-2105/3/8

Depends: altree
Homepage: http://claire.bardel.free.fr/software.html
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
License: GPL
WNPP: 461506
Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#altree
Pkg-Description: program to perform phylogeny based analyses
 This software was designed to perform phylogeny based analysis: first,
 it allows the detection of an association between a candidate gene and
 a disease, and second, it enables to make hypothesis about the
 susceptibility loci.

Depends: treeplot
Homepage: http://www.pge.cnrs-gif.fr/bioinfo/treeplot/
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
License: GPL
WNPP: 461506
Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treeplot
Pkg-Description: Phylogenetic tree file converter
 Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to
 Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic
 (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language
 (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map
 file (.pnm)

Depends: treevolve
Homepage: http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
License: has to be verified
WNPP: 461510
Pkg-URL: http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treevolve
Pkg-Description: simulation of evolution of DNA sequences
 treevolve will simulate the evolution of DNA sequences under a
 coalescent model, which allows exponential population growth,
 population subdivision according to an island model, migration and
 recombination. In addition different periods of population dynamics
 can be enforced at different times. For example, a period of
 exponential growth can be followed by a period of stasis where the
 population is subdivided into demes. Multiple sets of such simulated
 sequence data can then be compared to sequence data sampled from a
 population of interest using suitable statistics, and various
 evolutionary hypotheses concerning the evolution of this population
 tested.
 .
 Citation: Population dynamics of HIV-1 inferred from gene sequences
 Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.

Depends: infernal
Homepage: http://infernal.janelia.org/
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL
WNPP: 441840
Pkg-URL: http://packages.debian.org/source/experimental/infernal
Pkg-Description: RNA sequence comparison
 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence
 databases for RNA structure and sequence similarities. It is an
 implementation of a special case of profile stochastic context-free
 grammars called covariance models (CMs). A CM is like a sequence
 profile, but it scores a combination of sequence consensus and RNA
 secondary structure consensus, so in many cases, it is more capable of
 identifying RNA homologs that conserve their secondary structure more
 than their primary sequence.
 .
 The tool is an integral component of the Rfam database.
 .
 Users of this package should cite:
 "Query-Dependent Banding (QDB) for Faster RNA Similarity Searches."
  E. P. Nawrocki, S. R. Eddy. PLoS Comput. Biol., 3:e56, 2007.

Depends: mauve
Homepage: http://asap.ahabs.wisc.edu/mauve/
Responsible: Andreas Tille <tille@debian.org>
License: GPL
WNPP: 
Pkg-Description: multiple genome alignment
 Mauve is a system for efficiently constructing multiple genome alignments
 in the presence of large-scale evolutionary events such as rearrangement
 and inversion. Multiple genome alignment provides a basis for research
 into comparative genomics and the study of evolutionary dynamics.  Aligning
 whole genomes is a fundamentally different problem than aligning short
 sequences.
 .
 Mauve has been developed with the idea that a multiple genome aligner
 should require only modest computational resources. It employs algorithmic
 techniques that scale well in the amount of sequence being aligned. For
 example, a pair of Y. pestis genomes can be aligned in under a minute,
 while a group of 9 divergent Enterobacterial genomes can be aligned in
 a few hours.
 .
 Mauve computes and interactively visualizes genome sequence comparisons.
 Using FastA or GenBank sequence data, Mauve constructs multiple genome
 alignments that identify large-scale rearrangement, gene gain, gene loss,
 indels, and nucleotide substutition.
 .
 Mauve is developed at the University of Wisconsin.
 .
 Note: There are instructions for compiling Mauve from source available at
 http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html

Depends: asap
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille@debian.org>
License: GPL
WNPP: 
Pkg-Description: organize the data associated with a genome
 Developments in genome-wide approaches to biological research have
 yielded greatly increased quantities of data, necessitating the cooperation
 of communities of scientists focusing on shared sets of data. ASAP
 leverages the internet and database technologies to meet these needs.
 ASAP is designed to organize the data associated with a genome from the
 early stages of sequence annotation through genetic and biochemical
 characterization, providing a vehicle for ongoing updates of the annotation
 and a repository for genome-scale experimental data. Development was
 motivated by the need to more directly involve a greater community of
 researchers, with their collective expertise, in keeping the genome
 annotation current and to provide a synergistic link between up-to-date
 annotation and functional genomic data. The system is continually under
 development at the Genome Evolution Lab with the stable, in-use, publicly
 available University of Wisconsin installation updated regularly.
 .
 Software development on ASAP began in early 2002, and ASAP has been
 continually improved up until the present day. A longstanding goal of
 the ASAP project was to make the source code of ASAP available so that
 other installations of ASAP could be implemented. As future ASAP
 installations come to pass, ASAP will be further extended to be
 inter-operable between sites.

Depends: emboss-kaptain
Homepage: http://userpage.fu-berlin.de/~sgmd/download.html
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
License: GPL-2+
WNPP: 466682
Pkg-Description: graphical interface to EMBOSS using Kaptain
 EMBOSS.kaptn is a graphical user interface (GUI) for more than 200
 programms of the EMBOSS sequence analysis package. It uses Kaptain, a
 universal front-end for command line applications. EMBOSS is a
 collection of high-quality free Open Source software for sequence
 analysis.  With EMBOSS.kaptn it integrates nicely into X window based
 desktops like KDE.

Depends: agdbnet
Homepage: http://pubmlst.org/software/database/agdbnet/
Responsible: Andreas Tille <tille@debian.org>
License: GPL
WNPP:
Pkg-Description: antigen sequence database software for web-based bacterial typing
 AgdbNet is antigen sequence database software for web-based bacterial
 typing. The software facilitates simultaneous BLAST querying of multiple
 loci using either nucleotide or peptide sequences. It's written in Perl
 and runs on Linux/UNIX systems.
 .
 Databases are described by XML files and can have any number of loci, which
 may be defined by nucleotide and/or peptide sequences. The databases can
 optionally have integral isolate tables so that information about representative
 isolates can be retrieved or they may be configured to query external isolate
 databases, such as those hosted on PubMLST.org.
 .
 The software is used on a number of public bacterial typing databases:
  * Neisseria PorA variable regions | PorB | FetA
  * Campylobacter flaA
  * Streptococcus equi seM

Depends: gamgi
Homepage: http://www.gamgi.org/
Responsible: Steffen Moeller <moeller@debian.org>
License: Free
WNPP: 465994
Pkg-Description: general atomistic modelling graphic interface
 GAMGI provides a graphical user interface for the handling
 of molecular structures.

Depends: bioconductor
Homepage: http://www.bioconductor.org/
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL/LGPL
Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/bioconductor/
Pkg-Description: analysis and comprehension of genomic data
 Bioconductor is an open source and open development software project
 to provide tools for the analysis and comprehension of genomic data.
 .
 The Bioconductor core team is based primarily at the Biostatistics Unit of
 the Dana Farber Cancer Institute at the Harvard Medical School/Harvard School
 of Public Health. Other members come from various US and international
 institutions.
 .
 The broad goals of the projects are to
  * provide access to a wide range of powerful statistical and graphical methods
    for the analysis of genomic data;
  * facilitate the integration of biological metadata in the analysis of
    experimental data: e.g. literature data from PubMed, annotation data from
    LocusLink;
  * allow the rapid development of extensible, scalable, and interoperable
    software;
  * promote high-quality documentation and reproducible research;
  * provide training in computational and statistical methods for the analysis
    of genomic data.

Depends: biomart
Homepage: http://www.ebi.ac.uk/biomart/
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL
Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/martj/
Pkg-Description: distributed data integration system for biological data
 BioMart is a simple, distributed data integration system with
 powerful query capabilities. The BioMart data model has been applied
 to the following data sources: UniProt Proteomes, Macromolecular
 Structure Database (MSD), Ensembl, Vega, and dbSNP.
       
Depends: cluster3
Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
License: non-free
Responsible: Steffen Moeller <moeller@debian.org>
Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/cluster3/
Pkg-Description: find clustering solutions for genome data
 Cluster 3.0 is an enhanced version of Cluster, which was originally
 developed by Michael Eisen while at Stanford University. The main
 improvement consists of the k-means algorithm, which now includes
 multiple trials to find the best clustering solution. This is crucial
 for the k-means algorithm to be reliable. The routine for self-organizing
 maps was extended to include 2D rectangular geometries. The Euclidean
 distance and the city-block distance were added to the available
 measures of similarity.

Depends: jmol
Homepage: http://jmol.sourceforge.net/
Responsible:
License: LGPL
Pkg-URL: http://debian.wgdd.de/debian/dists/unstable/contrib/binary-all/science/
Pkg-Description: molecule viewer
 Jmol is a free, open source molecule viewer for students, educators,
 and researchers in chemistry and biochemistry.
  * The JmolApplet is a web browser applet that can be integrated into web pages.
  * The Jmol application is a standalone Java application that runs on the
    desktop.
  * The JmolViewer is a development tool kit that can be integrated into other
    Java applications.

Depends: jtreeview
Homepage: http://jtreeview.sourceforge.net/
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL
Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/treeview/
Pkg-Description: viewer for microarray data
 Java TreeView is an extensible viewer for microarray data in
 PCL or CDT format.

Depends: smile
Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL
Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/smile/
Pkg-Description: infer motifs in a set of sequences
 SMILE is a tool that infers motifs in a set of sequences, according to some
 criteria. It was first made to infer exceptional sites as binding sites in
 DNA sequences. Since the 1.4 version, it allows to infer motifs written on
 any alphabet (even degenerate) in any kind of sequences.
 .
 The specificity of SMILE is to allow to deal with what we call structured
 motifs, which are motifs associated by some distance constraints.

Depends: cactus
Homepage: http://www.cactuscode.org/Community/Biology.html
License: GPL
Pkg-Description:
 Cactus is an open source problem solving environment designed for scientists
 and engineers. Its modular structure easily enables parallel computation
 across different architectures and collaborative code development between
 different groups.
 .
 Cactus provides easy access to many cutting edge software technologies being
 developed in the academic research community, including the Globus
 Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
 adaptive mesh refinement, web interfaces, and advanced visualization tools.

Depends: contralign
Homepage: http://contra.stanford.edu/contralign/
License: Public Domain
Pkg-Description: parameter learning framework for protein pairwise sequence alignment
 CONTRAlign is an extensible and fully automatic parameter learning
 framework for protein pairwise sequence alignment based on pair
 conditional random fields. The CONTRAlign framework enables the
 development of feature-rich alignment models which generalize well to
 previously unseen sequences and avoid overfitting by controlling model
 complexity through regularization.

Depends: galaxy
Homepage: http://g2.trac.bx.psu.edu/
License: MIT
Pkg-Description: manipulate sequences and annotation files
 Galaxy is a web-based tool allowing users to perform operations which
 are usually done with command-line interface. Using galaxy, one can
 manipulate sequences and annotation files in many formats. Galaxy has
 strong ties with the UCSC genome browser, and makes it easy to
 visualise modified annotation files as a custom track.

Depends: genographer
Homepage: http://hordeum.oscs.montana.edu/genographer/
License: GPL
Pkg-Description: read data and reconstruct them into a gel image
 This program will read in data from an ABI 3700, 3100, 377 or 373,
 CEQ 2000 or SCF and reconstruct them into a gel image which is
 straightened and sized. Bins can be defined easily and viewed as
 thumbnails, which allows for a fairly quick and easy way of scoring a gel.
 .
 The program is written in Java and uses the Java 1.3 API. Therefore,
 it should run on any machine that can run java.

Depends: molekel
Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
License: GPL
Pkg-Description: multiplatform molecular visualization
 Molekel is an opensource (GPL) multiplatform molecular visualization
 program being developed at the Swiss National Supercomputing Centre
 (CSCS).

Depends: pftools
Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
License: GPL
Pkg-Description: tools to handle patterns from PROSITE
 ps_scan is a perl program used to scan one or several patterns, rules
 and/or profiles from PROSITE against one or several protein sequences
 in Swiss-Prot or FASTA format. It requires two compiled external
 programs from the PFTOOLS, which are also distributed with the sources.

Depends: proalign
Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
License: GPL
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
WNPP: 378290
Pkg-Description: Probabilistic multiple alignment program
 ProAlign performs probabilistic sequence alignments using hidden Markov
 models (HMM). It includes a graphical interface (GUI) allowing to (i)
 perform alignments of nucleotide or amino-acid sequences, (ii) view the
 quality of solutions, (iii) filter the unreliable alignment regions and
 (iv) export alignments to other softwares.
 .
 ProAlign uses a progressive method, such that multiple alignment is
 created stepwise by performing pairwise alignments in the nodes of a
 guide tree. Sequences are described with vectors of character
 probabilities, and each pairwise alignment reconstructs the ancestral
 (parent) sequence by computing the probabilities of different
 characters according to an evolutionary model. It has been published in
 Bioinformatics. 2003 Aug 12;19(12):1505-13.

Depends: ssaha
Homepage: http://www.sanger.ac.uk/Software/analysis/SSAHA/
License: GPL
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
WNPP: 425111
Pkg-Description: Sequence Search and Alignment by Hashing Algorithm
 SSAHA is a software tool for very fast matching and alignment of DNA
 sequences. It achieves its fast search speed by converting sequence
 information into a `hash table' data structure, which can then be
 searched very rapidly for matches. It was published by Ning Z,
 Cox AJ, Mullikin JC in Genome Res. 2001;11;1725-9.
 .
 SSAHA is the only free software of its category (fast search of nearly
 indentical sequences). The popular alternative, BLAT, is restricted to
 non-commercial use.

Depends: ngila
Homepage: http://scit.us/projects/ngila/
License: GPLv3
Responsible: Charles Plessy <charles-debian-nospam@plessy.org>
WNPP: 439996
Pkg-Description: global pairwise alignments with logarithmic and affine gap costs
 Ngila is an application that will find the best alignment of a pair
 of sequences using log-affine gap costs, which are the most
 biologically realistic gap costs.
 .
 Ngila implements the Miller and Myers (1988) algorithm in order to
 find a least costly global alignment of two sequences given homology
 costs and a gap cost. Two versions of the algorithm are
 included: holistic and divide-and-conquer. The former is faster but
 the latter utilizes less memory. Ngila starts with the
 divide-and-conquer method but switches to the holistic method for
 subsequences smaller than a user-established threshold. This improves
 its speed without substantially increasing memory requirements. Ngila
 also allows users to assign costs to end gaps that are smaller than
 costs for internal gaps. This is important for aligning using the
 free-end-gap method.
 .
 Ngila is published in Cartwright RA Bioinformatics 2007
 23(11):1427-1428; doi:10.1093/bioinformatics/btm095

Depends: tm-align
Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
License: free to change and redistribute
Responsible: Steffen Moeller <moeller@debian.org>
WNPP: 447505
Pkg-Description: structural protein alignment
 TM-align is a structural alignment program for comparing two proteins
 whose sequences can be different. TM-align will first find the best
 equivalent residues of two proteins based on the structure similarity
 and then output a TM-score.
 .
 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
Homepage: http://staden.sourceforge.net/
License: BSD
Pkg-Description: DNA sequence assembly (Gap4), editing and analysis tools
 A fully developed set of DNA sequence assembly (Gap4), editing and
 analysis tools (Spin).
