Task: Biology
Description: Debian Med micro-biology packages
 This metapackage will install Debian packages related to molecular biology,
 structural biology and bioinformatics for use in life sciences.

X-Begin-Category: Phylogenetic analysis

Depends: altree

Depends: beast-mcmc

Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle

Depends: probalign

Depends: treeviewx

Depends: figtree

Depends: spread-phy

X-End-Category: Phylogenetic analysis

Depends:     phylip
Why:         Phylogenetic analysis (Non-free, thus only suggested).

X-Comment: treetool is removed from Debian because it is not maintained upstream since
 1995 and cause the Xserver to freeze under Squeeze

Depends:     fastlink, loki, plink, r-cran-qtl, r-cran-genabel
Why:         Genetics

X-Begin-Category: Sequence alignments and related programs.

Depends:     amap-align
Remark: Dead upstream
 The homepage of this project vanished as well as the Download area.  An
 old unmaintained version remained at code.google.com.  Please drop the
 maintainer a note if you have any news of this project.

Depends:     boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise

Depends:     maqview

Depends: bwa

Depends: mummer

Depends: blast2

Depends: ncbi-blast+

Depends: mafft

Depends: sra-toolkit

Depends: t-coffee

Depends: kalign

Depends: hmmer

Depends: exonerate

Depends: dialign

Depends: dialign-tx

Depends: poa

Depends: probcons

Depends: proda

Depends: seaview

Depends: sigma-align

Depends: emboss

Depends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
Suggests:    emboss-explorer
Why:         The EMBOSS sequence analysis suite and its galaxy.

Depends:     arb
Why:         Sequence alignments and related programs (Non-free, thus only suggested).

Depends: clustalx, clustalo

Depends: clustalw | clustalw-mpi

Depends: mothur, bowtie, bowtie2

Depends: transtermhp

X-End-Category: Sequence alignments and related programs.

X-Begin-Category: high-throughput sequencing

Depends: last-align, maq, ssake, velvet

Depends: qiime

X-End-Category: high-throughput sequencing

X-Begin-Category: Analysis of RNA sequences.

Depends: infernal

Depends: rnahybrid
X-Category: Target duplex prediction

X-End-Category: Analysis of RNA sequences.

X-Begin-Category: Molecular modelling and molecular dynamics

Depends:     adun.app

Depends:     garlic, gamgi, gdpc, ghemical, jmol, pymol, r-other-bio3d, massxpert
Comment:     r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team

Depends: gromacs

Depends: rasmol

Depends: modeller
Homepage: http://salilab.org/modeller/
Pkg-URL: http://salilab.org/modeller/release.html#deb
Remark: The package is created independently from Debian Med or Debian Science.
Pkg-Description: MODELLER provides three dimensional structures of proteins by satisfaction
  of spatial constraints. The program comes as closed source, only free for academia,
  see http://salilab.org/modeller/registration.html.

X-End-Category: Molecular modelling and molecular dynamics

Depends:     plasmidomics
Why:         Presentation

X-Begin-Category: Tools for the molecular biologist.

Depends:     gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer

Depends: melting

Suggests: melting-gui
Comment: I think it makes sense to point users to GUI applications as well as to
 the console applications - in this case melting (Andreas Tille)

Depends: mipe

Depends: primer3

X-End-Category: Tools for the molecular biologist.

X-Begin-Category: Genome Browser

Depends: gbrowse
X-Importance: Academic ones are really expensive for commercial use

X-End-Category: Genome Browser

Depends: biomaj

Suggests: biomaj-watcher

Ignore: mozilla-biofox
Remark: biofox was removed from Debian (see #727689)
 The bug log (http://bugs.debian.org/727689) explains the reasons for
 the removal.  Please keep us informed if you become aware about
 upstream changes that enable using this plugin for firefox >= 10.

Depends:     glam2
Why:         Motif search

Depends: raster3d

Depends: phyml

Depends: autodock
Registration: http://autodock.scripps.edu/downloads/autodock-registration
Why:         Molecular modelling and molecular dynamics.

Depends: autogrid

Depends: autodock-vina

Depends: autodocktools
Comment: The package autodocktools depends from the mgltools-* packages mentioned
         above, so they will be installed even if they would not be mentioned in
         the list of Depends in the metapackage med-bio.  But leaving them out here
         would hide them from the tasks and bugs list as well from the sectioning in
         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.
 .
         This was changed by adding Enhances field to the packages in question.

Depends: mustang

Depends: probabel

Depends: theseus

Depends: staden-io-lib-utils

Depends: samtools, bedtools, filo

Depends: gassst

Depends: r-bioc-hilbertvis
Remark: It would be interesting to package HilbertVisGUI (see below) as well.

Depends: r-other-mott-happy.hbrem

Depends: seq-gen

Depends: snp-sites

Depends: mira-assembler

Depends: alien-hunter

Depends: seqan-apps

Depends: ncoils

Depends: gentle

Depends: gmap

Depends: igv

Depends: picard-tools

Depends: acedb-other-dotter, acedb-other-belvu, acedb-other

Depends: python-cogent

Depends: paml

Depends: velvetoptimiser

Depends: ensembl
Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/
Remark: Ensembl was removed from Debian due #645487
 Ensembl used to be in Debian experimental branch but was removed for formal reasons which
 are explained in http://bugs.debian.org/645487

Depends: mrbayes

Depends: pdb2pqr

Depends: squizz

Depends: clonalframe

Depends: dssp

Depends: jellyfish

Depends: ballview

Depends: pynast

Depends: raxml

Depends: mlv-smile

Suggests: cain

Depends: cd-hit

Depends: cufflinks

Depends: r-bioc-cummerbund

Depends: eigensoft

Depends: grinder

Depends: jalview

Depends: reprof

Depends: tm-align

Depends: norsnet

Depends: norsp

Depends: predictnls

Depends: prime-phylo

Depends: proftmb

Depends: profbval

Depends: profisis

Depends: hhsuite

Depends: ffindex

Depends: flexbar

Depends: blimps-utils

Depends: sift

Depends: neobio

Depends: ray

Depends: ugene

Depends: logol-bin

Depends: soapdenovo, soapdenovo2

Depends: microbiomeutil, chimeraslayer, nast-ier, wigeon

Depends: minia

Depends: trimmomatic

Depends: saint

Depends: rtax

Depends: rate4site

Depends: topp, openms

X-Mark: Prospective packages are starting here.

X-Mark: Packages in Vcs - Information about these is queried from UDD as well

Depends: acacia

Depends: arden

Depends: biceps
Remark: Mentioned at http://www.renard.it/, developed in RKI

Depends: emperor

Depends: fitgcp

Depends: gasic

Depends: giira

Depends: ipig

Depends: aevol

Depends: amos-assembler, hawkeye
Language: Perl

Depends: anfo

Depends: apollo

Depends: aragorn

Depends: axparafit, axpcoords

Depends: bamtools

Depends: bagpipe

Depends: bigsdb

Depends: bitseq

Depends: blat

Depends: cassiopee

Depends: cdbfasta

Depends: cinema
Language: Java

Depends: clearcut

Depends: clonalorigin

Depends: cluster3

Depends: crac

Depends: crossbow
X-Category: Sequencing

Depends: cytoscape

Depends: dazzle

Depends: ecell

Depends: edtsurf

Depends: emmax

Depends: fasttree

Depends: fastaq

Depends: fastqc

Depends: unc-fish

Depends: forester
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-amd64
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 BioLinux was following the upstream name change to archaeopteryx and thus the
 package is called bio-linux-archaeopteryx there.
 .
 The binary package is full of JARs without source.

Depends: freecontact

Depends: freebayes

Depends: fsa
Enhances: t-coffee
Remark: Precondition for T-Coffee
 see http://wiki.debian.org/DebianMed/TCoffee

Depends: genometools

Depends: grabix

Depends: grogui

Depends: haploview

Depends: hmmer2
Remark: This older version of HMMER is used in some applications
 While Debian has HMMER 3 since some time there are users of
 HMMER 2 interested in having this old version available and
 thus the package is reintroduced.

Depends: idba

Depends: jbrowse

Depends: kempbasu

Depends: kissplice

Depends: lagan
X-Category: Comparative genomics

Depends: ltrsift

Depends: logomat-m

Depends: kclust

Depends: mach-haplotyper

Depends: macs

Depends: mage2tab

Depends: martj

Depends: mauvealigner
Pkg-URL: http://people.debian.org/~tille/packages/mauvealigner/
Language: C++ and Java
X-Category: Multiple genome alignment
X-Importance: efficient
Remark: 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: meme
License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html)

Depends: metastudent

Depends: molekel

Depends: mosaik-aligner

Depends: mpsqed

Depends: mrs

Depends: mugsy

Depends: murasaki

Depends: ncbi-seg

Depends: ngila

Depends: ngsqctoolkit

Depends: nw-align

Depends: oases

Depends: pal2nal

Depends: paraclu

Depends: parsinsert

Depends: patman

Depends: patristic
Language: Java

Depends: pcma
Remark: Precondition for T-Coffee
 see http://wiki.debian.org/DebianMed/TCoffee
 .
 Check with authors about licensing, they adopted code from clustalw which is now
 free.  Thus a change might be possible

Depends: perm

Depends: phyloviz-core
Remark: There are several plugins to package
 The download page http://www.phyloviz.net/wiki/plugins/ lists several plugins
 that should be packaged (single or as bundle) as well.

Depends: phyutility

Depends: plato

Depends: prank

Depends: predictprotein

Depends: proalign

Depends: prodigal

Depends: pscan-tfbs

Depends: psipred

Depends: pycorrfit

Depends: pyscanfcs

Depends: python-reaper

Depends: r-bioc-rtracklayer, r-bioc-gviz, r-bioc-biostrings

Suggests: r-cran-boolnet

Depends: r-cran-vegan

Depends: relion-gui, relion-bin | relion-bin-mpi

Depends: r-other-valdar-bagphenotype.library

Depends: rdp-classifier
Remark: Needs ReadSeq as Dependency
 The source contains a prebuilded JAR of
 http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
 which needs to be packaged first.

Depends: rosetta

Depends: sap
Remark: Precondition for T-Coffee
 see http://wiki.debian.org/DebianMed/TCoffee

Depends: sga

Depends: seqtk

Depends: sequenceconverter.app
Remark: Formerly part of Debian as biococoa.app but removed
 The package was part of Debian under the name biococoa.app which is confusing
 because biococoa is actually a library for working with sequences under GNUstep.
 There was an attempt to reupload under the name sequenceconverter.app but
 ftpmaster did not accepted the package.  The reasons can be read here:
 http://lists.alioth.debian.org/pipermail/debian-med-packaging/2009-May/003430.html
 .
 Version 1.6 is the last upstream version that works with GNUstep.  If
 newer versions are needed to work under Linux try to convince upstream to
 support GNUstep.

Depends: situs

Depends: smalt
Remark: This can be regarded as successor of ssaha2
 This program is from the same author as ssaha2 and according to its author
 faster and more precise than ssaha2 (except for sequences > 2000bp).

Depends: snpeff

Depends: spades

Depends: ssaha
Remark: Successor for ssaha2 available: smalt
 The program smalt is from the same author is according to its author
 faster and more precise than ssaha2 (except for sequences > 2000bp)

Depends: staden

Depends: strap, strap-base
Language: Java

Depends: tacg
X-Category: Motif detection
X-Importance: powerful

Depends: treeview
X-Category: Visualisation

X-Depends: treevolve
X-Comment: Homepage of software vanished, packaging in SVN is obviosely stalled
 Feel free to delete the 'X-' in front if you intend to do something on this package

Depends: uc-echo
X-Category: NGS

Depends: varscan

Depends: vienna-rna
X-Category: Secondary structure of nucleic acids

Depends: vmd

Depends: wgs-assembler
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Depends: zalign

Depends: zodiac-zeden
Language: C, C++

Depends: discosnp, mapsembler2

Depends: dnaclust

X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here

Depends: 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
 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: 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: asap
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille@debian.org>
License: GPL
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.
X-Category: Annotation

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: concavity
Homepage: http://compbio.cs.princeton.edu/concavity/

Depends: conservation-code
Homepage: http://compbio.cs.princeton.edu/conservation/
WNPP: 690058

Depends: galaxy
Homepage: http://g2.trac.bx.psu.edu/
License: MIT
WNPP: 432472
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: pftools
Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
License: GPL
Pkg-Description: tools to handle profiles of protein domains from PROSITE
 The 'pftools' package is a collection of experimental programs
 supporting the generalized profile format and search method of
 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.
 .
 Also seen on http://www.isrec.isb-sib.ch/profile/profile.html
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
License: GPL
X-Category: Graphical representation of sequence conservation
Language: Tcl/Tk
Pkg-Description: Graph Visualization Tool
 PhyloGrapher is a program designed to visualize and study evolutionary
 relationships within families of homologous genes or proteins
 (elements).  PhyloGrapher is a drawing tool that generates custom graphs
 for a given set of elements. In general, it is possible to use
 PhyloGrapher to visualize any type of relations between elements.
 Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
 the results of a BLAST search as a graph.
 .
 PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
 biological sequence alignment reports (BLAST is provided by Debian's
 blast2 package).
Remark: Outdated upstream, better alternatives available
 The former packaging effort of this package was dropped.  It seems
 that http://cytoscape.org/ is a reasonable replacement.

Depends: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
WNPP: 395840
License: unknown
Pkg-Description: Graphical interface for molecular phylogenetic inference
 Phylo_win is a graphical colour interface for molecular phylogenetic
 inference. It performs neighbor-joining, parsimony and maximum
 likelihood methods and bootstrap with any of them. Many distances can be
 used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
 (1995), LogDet for nucleotidic sequences, Poisson correction for protein
 sequences, Ka and Ks for codon sequences. Species and sites to include
 in the analysis are selected by mouse. Reconstructed trees can be drawn,
 edited, printed, stored and evaluated according to numerous criteria.
 .
 This program uses sources files from the Phylip program, which forbids
 its use for profit.  Therfore, Phylo_win will unfortunately have to be
 distributed in contrib or non-free.
Remark: Issuer of previous ITP said:
 Because I could never figure out the license of Phylo_win, and because the
 upstream authors released SeaView 4, which provides similar functionalities, I
 will not package Phylo_win.
 .
 Probably it makes sense to remove this project from the prospective packages
 list.

Depends: gbioseq
Homepage: http://www.bioinformatics.org/project/?group_id=94
License: GPL
Pkg-Description: DNA sequence editor for Linux
 gBioSeq is in an early stage of development, but it is already running.
 The goal is to provide an easy to use software to edit DNA sequences under
 Linux, Windows, MacOsX, using GTK C# (Mono).

Depends: 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
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
 TraceTuner is a DNA sequencing quality value, base calling and trace
 processing software application originally developed by Paracel,
 Inc. While providing a flexible interface and capability to adopt the
 "pure" base calls produced by Phred, KB or any other "original"
 caller, it offers competitive features not currently available in
 other tools, such as customized calibration of quality values,
 advanced heterozygote and mixed base calling and deconvolving the
 "mixed" electropherograms resulting from the presence of indels into
 a couple of "pure" electropherograms. Previous versions of TraceTuner
 were used by Celera Genomics to process over 27 million reads from
 both Drosophila and human genome projects and by Applied Biosystems,
 as a component of its SNP detection and genotyping software product
 SeqScape. TraceTuner implements an advanced peak processing
 technology for resolving overlapping peaks of the same dye color into
 individual, or "intrinsic" peaks. This technology was protected by US
 Patent #6,681,186. Currently, TraceTuner is an open source software,
 which has been used by J. Craig Venter Institute's DNA Sequencing and
 Resequencing pipelines.
 .
 The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All
 rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is
 being made available free of charge by Applera Corporation subject to the terms
 and conditions of the GNU General Public License, version 2, as published by the
 Free Software Foundation (the "GNU General Public License").

Depends: 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
 TWAIN is a new syntenic genefinder which employs a Generalized Pair
 Hidden Markov Model (GPHMM) to predict genes in two closely related
 eukaryotic genomes simultaneously.  It utilizes the MUMmer package to
 perform approximate alignment before applying a GPHMM based on an
 enhanced version of the TigrScan gene finder.  TWAIN was written by
 Bill Majoros and Mihaela Pertea while at The Institute for Genomic
 Research (TIGR).
 .
 TWAIN consists of two components: (1) ROSE, the Region Of Synteny
 Extractor, which identifies contiguous regions likely to contain one
 or more syntenic genes, and (2) OASIS, a generalized pair hidden
 Markov model (GPHMM) for predicting genes in the regions identified
 by ROSE.  The system utilizes approximate alignments constructed by
 the PROmer and NUCmer programs in the MUMmer package to assess
 approximate alignment scores efficiently.  More detailed information
 on the architecture of this system will be made available soon.
 Slides from a talk at Computational Genomics 2004 are now available.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Depends: rose
Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html
License: Open Source
Pkg-Description: Region-Of-Synteny Extractor
 ROSE is a program which identifies regions between two genomes which
 are likely to contain orthologous genes. The two genomes are given as
 two multi fasta files of DNA sequences. The PROmer program from the
 MUMmer package needs to be run first between the two genomes, and the
 resulting delta file is then input to ROSE. If a previous annotation
 is available for one or both genomes, then the coordinates of the
 annotated genes from a genome can be optionally given as input in a
 gff file. The gene coordinates will be used to guide the length of
 the regions produced by ROSE. By default, when finding a region of
 consistent alignments, ROSE will add a user-defined margin (1000 bp
 by default) on either side of that region. When a predicted gene
 overlaps an alignment we use the gene prediction to extend the
 boundaries of the output region.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Depends: glimmerhmm
Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/
License: Artistic
Pkg-Description: Eukaryotic Gene-Finding System
 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov
 Model (GHMM). Although the gene finder conforms to the overall
 mathematical framework of a GHMM, additionally it incorporates splice
 site models adapted from the GeneSplicer program and a decision tree
 adapted from GlimmerM. It also utilizes Interpolated Markov Models
 for the coding and noncoding models . Currently, GlimmerHMM's GHMM
 structure includes introns of each phase, intergenic regions, and
 four types of exons (initial, internal, final, and single). A basic
 user manual can be consulted here.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Depends: genezilla
Homepage: http://www.genezilla.org/
License: Artistic
Language: C++
X-Importance: state-of-art
X-Category: Gene prediction (through GHMM)
Pkg-Description: eukaryotic gene finder
 GeneZilla is a state-of-the-art program for computational prediction
 of protein-coding genes in eukaryotic DNA, and is based on the
 Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN
 and GENIE. It is highly reconfigurable and includes software for
 retraining by the end-user. It is written in highly optimized C++ and
 runs under most UNIX/Linux platforms. The run time and memory
 requirements are linear in the sequence length, and are in general
 much better than those of competing systems, due to GeneZilla's novel
 decoding algorithm. Graph-theoretic representations of the high
 scoring open reading frames are provided, allowing for exploration of
 sub-optimal gene models. It utilizes Interpolated Markov Models
 (IMMs), Maximal Dependence Decomposition (MDD), and includes states
 for signal peptides, branch points, TATA boxes, CAP sites, and will
 soon model CpG islands as well.
 .
 GeneZilla is an open-source project hosted at bioinformatics.org and
 currently consists of ~20,000 lines of code.  GeneZilla evolved out
 of the ab initio eukaryotic gene finder TIGRscan, which was developed
 at The Institute for Genomic Research over a 3-year period under NIH
 grants R01-LM06845 and R01-LM007938, and which served as the basis
 for the comparative gene finder TWAIN.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Depends: exalt
Homepage: http://www.cbcb.umd.edu/software/exalt/
License: Artistic
Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
 ExAlt is a software program designed to predict alternatively spliced
 overlapping exons in genomic sequence. The program works in several
 ways depending on the available input. ExAlt can use information of
 existing gene structure as well as sequence conservation to improve
 the precision of it's predictions. ExAlt can also make predictions
 when only a single genomic sequence is available. ExAlt has been
 extensively tested on Drosophila melanogaster, but can be adapted to
 run on other species.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Depends: jigsaw
Homepage: http://www.cbcb.umd.edu/software/jigsaw/
License: Artistic
Pkg-Description: gene prediction using multiple sources of evidence
 JIGSAW is a program designed to use the output from gene finders,
 splice site prediction programs and sequence alignments to predict
 gene models. The program provides an automated way to take advantage
 of the many succsessful methods for computational gene prediction and
 can provide substantial improvements in accuracy over an individual
 gene prediction program.
 .
 JIGSAW is available for all species. It is tested on Human, Rice
 (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus
 neoformans, Entamoeba histolytica, Theileria parva, Aspergillus
 fumigatus, Plasmodium falciparum and Plasmodium yoelii.
 .
 The linear combiner option is now available in the current JIGSAW
 software distribution. This allows JIGSAW to be run without the use
 of training data. A weight is assigned to each evidence source, and
 gene predictions are based on a weighted voting scheme, yielding the
 best 'consensus' predictions.
 .
 Predictions are now available for the ENCODE regions in Human and
 viewable as custom tracks in the UCSC Human Genome
 Browser. Predictions available for the Human genome and viewable as
 custom tracks in the UCSC Human Genome Browser
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Depends: genesplicer
Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/
License: Artistic
Pkg-Description: computational method for splice site prediction
 A fast, flexible system for detecting splice sites in the genomic DNA
 of various eukaryotes. The system has been trained and tested
 successfully on Plasmodium falciparum (malaria), Arabidopsis
 thaliana, human, Drosophila, and rice . Training data sets for human
 and Arabidopsis thaliana are included. Use the GeneSplicer Web
 Interface to run GeneSplicer directly, or see below for instructions
 on downloading the complete system including source code.
 .
 There is no independent program to train GeneSplicer, but there is a
 way to obtain the necessary files by using the training procedure of
 GlimmerHMM.
Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/)

Ignore: riso
Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html
License: not specified
Pkg-Description: motif discovery tool
 RISO discovers motifs composed of many binding sites separated by
 spacers. Each binding site is called a box
 .
 The author of SMILE claims at his homepage
 http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is
 faster and more powerfull than SMILE which is described itself as
 "SMILE is a tool that infers motifs in a set of sequences, according
 to some criterias. It was first made to infer exceptionnal sites as
 binding sites in DNA sequences. 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. In particular, SMILE is able to group under a unique
 model different occurrences composed of several boxes separated by
 spacers of different lengths."
 .
 The reference to SMILE is made here especially because there is some
 work done in the Debian Med SVN at
 http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/
 .
 On the other hand the SMILE author told us in private mail that he
 thinks that RISO is dead and SMILE continues to have some importance.

Depends: mummergpu
Homepage: http://mummergpu.sourceforge.net/
License: Artistic
Pkg-Description: High-throughput sequence alignment using Graphics Processing Units
 The recent availability of new, less expensive high-throughput DNA
 sequencing technologies has yielded a dramatic increase in the volume
 of sequence data that must be analyzed. These data are being
 generated for several purposes, including genotyping, genome
 resequencing, metagenomics, and de novo genome assembly
 projects. Sequence alignment programs such as MUMmer have proven
 essential for analysis of these data, but researchers will need ever
 faster, high-throughput alignment tools running on inexpensive
 hardware to keep up with new sequence technologies.
 .
 MUMmerGPU is a low cost, ultra-fast sequence alignment program
 designed to handle the increasing volume of data produced by new,
 high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in
 replacement for MUMmer, using the GPUs in common workstations to
 simultaneously align multiple query sequences against a single
 reference sequence stored as a suffix tree. By processing the queries
 in parallel on the highly parallel graphics card, MUMmerGPU achieves
 more than a 10-fold speedup over a serial CPU version of the sequence
 alignment kernel, and outperforms MUMmer on a high end CPU by
 3.5-fold in total application time when aligning reads from recent
 sequencing projects using Solexa/Illumina, 454, and Sanger sequencing
 technologies.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Depends: amoscmp
Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html
License: Artistic
Pkg-Description: comparative genome assembly package
 A comparative assembler is a program that can assemble a set of
 shotgun reads from an organism by mapping them to the finished
 sequence of a related organism. Thus, a comparative assembler
 transforms the traditional overlap-layout-consensus approach to
 alignment-layout-consensus. The AMOScmp package uses the MUMmer
 program to perform a mapping of the reads to the reference genome,
 then processes the alignment results with a sophisticated layout
 program designed to take into account polymorphisms between the two
 genomes. For a detailed description of the algorithms involved please
 refer to the paper listed in the References section.
 .
 AMOScmp uses as AMOS messages as both the inputs and the outputs (see
 documentation). Two utilities are provided to process these files:
 tarchive2amos - a versatile converter from trace archive .seq, .qual,
 and .xml information into AMOS formatted data; amos2ace - a converter
 from AMOS formatted data to the .ACE assembly format. In addition,
 the AMOS::AmosLib Perl module is provided as a tool for users who
 prefer to write their own conversion utilities. Please see the
 documentation included with the distribution for more information.
 .
 AMOScmp is part of the AMOS package (see
 http://amos.sourceforge.net/)- a collaborative effort to develop a
 modular open-source framework for assembly development.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Depends: minimus
Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html
License: Artistic
Pkg-Description: AMOS lightweight assembler
 minimus is an assembly pipeline designed specifically for small
 data-sets, such as the set of reads covering a specific gene. Note
 that the code will work for larger assemblies (we have used it to
 assemble bacterial genomes), however, due to its stringency, the
 resulting assembly will be highly fragmented. For large and/or
 complex assemblies the execution of Minimus should be followed by
 additional processing steps, such as scaffolding.
 .
 minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules:
  * overlapper - computes the overlaps between the reads using a
    modified version of the Smith-Waterman local alignment algorithm
  * tigger - uses the read overlaps to generate the layouts of reads
    representing individual contigs
  * make-consensus - refines the layouts produced by the tigger to
    generate accurate multiple alignments within the reads
 .
 minimus uses as AMOS messages as both the inputs and the outputs (see
 documentation). Two utilities are provided to process these files:
 tarchive2amos - a versatile converter from trace archive .seq, .qual,
 and .xml information into AMOS formatted data; amos2ace - a converter
 from AMOS formatted data to the .ACE assembly format. In addition,
 the AMOS::AmosLib Perl module is provided as a tool for users who
 prefer to write their own conversion utilities. Please see the
 documentation included with the distribution for more information.
 .
 minimus is part of the AMOS package - a collaborative effort to
 develop a modular open-source framework for assembly development.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Ignore: catissuecore
Homepage: https://cabig.nci.nih.gov/tools/catissuecore
License: to be clarified, NCICB Open Source Project Site
Pkg-Description: biospecimen inventory, tracking, and basic annotation
 caTissue Core is caBIG's tissue bank repository tool for biospecimen
 inventory, tracking, and basic annotation. Version 1.2.1 of caTissue
 permits users to track the collection, storage, quality assurance,
 and distribution of specimens as well as the derivation and
 aliquotting of new specimens from an existing ones (e.g. for DNA
 analysis). It also allows users to find and request specimens that
 may then be used in molecular, correlative studies.
 .
 Intended Audiences: Translational Researchers, Pathologists, Biobank
 Managers
Note: A lot of stuff can be found at National Cancer Institute's
 Center for Bioinformatics (NCICB) Open Source Project Site
 http://gforge.nci.nih.gov/ which has to be evaluated and put into the
 right category of our tasks files

Ignore: trapss
Homepage: https://putt.eng.uiowa.edu/
License: Creative Commons for Science license
Pkg-Description: Transcript Annotation Prioritization and Screening System
 TrAPSS stands for Transcript Annotation Prioritization and Screening
 System. It is a system comprised of several tools written by
 researchers at the Coordinated Lab for Computational Genomics in the
 University of Iowa. The system aims to aid scientists who are
 searching for the genetic mutation or mutations that are linked to
 expression of a disease phentotype. The system offers support for
 almost all areas of a mutation discovery project from the creation
 and prioritization of a large candidate gene list, to the selection,
 ordering, and managing of primer pairs, and even support for SSCP
 assay results. TrAPSS is a currently deployed and often used tool for
 several laboratories here at the University of Iowa in the College of
 Medicine. The system is composed of several Java applications, many
 web-based PHP tools, and a local MySQL database. Even the Java
 applications are available through a web browser due to Sun's Java
 Web Start. Director of the CLCG, Professor Terry A. Braun, heads the
 project along with Dr. Todd Scheetz and Prof. Thomas
 L. Casavant. Eight developers create and maintain the software:
 Bartley Brown , Hakeem Almabrazi, Steven Davis and Jason Grundstad;
 along with three graduate students, Brian O'Leary, John Ritchison and
 Michael Smith; and one undergraduate student, Matthew Kemp.
 Importance of TrAPSS
 .
 The true importance of TrAPSS is that it is based upon a novel way to
 examine a large candidate list of genes. Rather than sequentially
 examining full genes, the scheme often followed in current target
 identification projects, TrAPSS provides tools that offer the user
 the opportunity to screen certain small parts of several genes from
 the candidate list at once. This "parallel" screening idea was
 envisioned by researchers here at the University of Iowa including
 Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate
 students Steven Davis and Brian O'Leary has demonstrated the
 advantage of the parallel screening method over the sequential
 sequencing of large candidate lists.
Note: Found at
 http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337

Depends: bambus
Homepage: http://amos.sourceforge.net/docs/bambus/
License: Artistic
Pkg-Description: hierarchical approach to building contig scaffolds
 BAMBUS is the first publicly available scaffolding program. It orders
 and orients contigs into scaffolds based on various types of linking
 information. Additionally, BAMBUS allows the users to build scaffolds
 in a hierarchical fashion by prioritizing the order in which links
 are used. For more information please check out the online
 documentation.
 .
 Note that currently Bambus is undergoing a transition in order to be
 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: gmv
Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV
License: GPL
Pkg-Description: comparative genome browser for Murasaki
 GMV is a comparative genome browser for Murasaki. GMV visualizes
 anchors from Murasaki, annotation data from GenBank files, and
 expression / prediction score from GFF files.

Depends: 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
Homepage: http://amos.sourceforge.net/Figaro/Figaro.html
License: Artistic
Pkg-Description: novel vector trimming software
 Figaro is a software tool for identifying and removing the vector
 from raw DNA sequence data without prior knowledge of the vector
 sequence.  By statistically modeling short oligonucleotide
 frequencies within a set of reads, Figaro is able to determine which
 DNA words are most likely associated with vector sequence.  For a
 description of Figaro's algorithms please see our paper.  Figaro is
 part of the AMOS suite.
Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)

Depends: mirbase
Homepage: http://microrna.sanger.ac.uk/
License: Public Domain
WNPP: 420938
Responsible: Charles Plessy <plessy@debian.org>
Pkg-Description: The microRNA sequence database
 The miRBase Sequence Database provides a searchable repository
 for published microRNA sequences and associated annotation,
 functionality previously provided by the microRNA Registry.  miRBase
 also contains predicted miRNA target genes in miRBase Targets, and
 provides a gene naming and nomenclature function in the miRBase
 Registry.
 .
 Release 9.1 of the database contains 4449 entries representing hairpin
 precursor miRNAs, expressing 4274 mature miRNA products, in primates,
 rodents, birds, fish, worms, flies, plants and viruses.
 .
 This package will install the miRBase database for mySQL, EMBOSS, and/or
 ncbi-blast if you have the corresponding packages installed.
 .
 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
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
 ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs
 sampler for finding motifs in a set of DNA or protein sequences. The
 program takes as input a set containing anywhere from a few dozen to
 thousands of sequences, and searches through them for the most common
 motif, assuming that each sequence contains one copy of the motif. We
 have used ELPH to find patterns such as ribosome binding sites (RBSs)
 and exon splicing enhancers (ESEs). See below for instructions on
 downloading the complete system, including source code.
 .
 An online tool that uses ELPH output for identifying exon splicing
 enhancers can be found at
 http://www.cbcb.umd.edu/software/SeeEse/index.html .
Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)

X-Depends: repeatfinder
X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/
X-License: Artistic
X-Pkg-Description: finding repetitive sequences complete and draft genomes
 Two programs for finding repeats in genomic DNA sequences.  The first
 program, described in the paper by Volfovsky et al. (2001) Genome
 Biology is RepeatFinder.  A second program, designed specifically to
 find repeats likely to confuse a genome assembly, is called
 ClosureRepeatFinder.  The two programs are quite different and have
 different purposes; RepeatFinder is intended to be the more
 comprehensive approach.  Note that RepeatFinder depends on Stefan
 Kurtz's REPuter.
X-Note: Depends from non-distributable code reputer (see below)

X-Depends: reputer
X-Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html
X-License: non-commercial
X-Pkg-Description: fast computation of maximal repeats in complete genomes
 A software tool was implemented that computes exact repeats and
 palindromes in entire genomes very efficiently.
X-Note: Code is not redistributable see mailing list discussion at
 http://lists.debian.org/debian-med/2012/07/msg00195.html

Depends: uniprime
Homepage: http://code.google.com/p/uniprime/
License: GPL-3+
Responsible: Charles Plessy <plessy@debian.org>
Pkg-Description: workflow-based platform for universal primer design
 UniPrime automatically designs large sets of universal primers by simply
 inputting a GeneID reference. It automatically retrieves and aligns
 orthologous sequences from GenBank, identifies regions of conservation within
 the alignment and generates suitable primers that can amplify variable genomic
 regions. UniPrime differs from previous automatic primer design programs in
 that all steps of primer design are automated, saved and are phylogenetically
 limited. We have experimentally verified the efficiency and success of this
 program. UniPrime is an experimentally validated, fully automated program that
 generates successful cross-species primers that take into account the
 biological aspects of the PCR.

Depends: genetrack
Homepage: http://sysbio.bx.psu.edu/genetrack.html
License: MIT
Responsible: Charles Plessy <plessy@debian.org>
Pkg-Description: genomic data storage and visualization framework
 GeneTrack is a high performance bioinformatics data storage and analysis
 system designed to store genome wide information. It is currently used to
 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
Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi
License: to be clarified
Pkg-Description: detect and analyze conserved gene pairs
 Comparison of complete microbial genomes reveals a large number of
 conserved gene clusters - sets of genes that have the same order in
 two or more different genomes. Such gene clusters often, but not
 always represent a co-transcribed unit, or operon. A method was
 developed to detect and analyze conserved gene pairs - pairs of genes
 that are located close on the same DNA strand in two or more
 bacterial genomes. For each conserved gene pair, an estimate of
 probability is calculated that the genes belong to the same
 operon. The algorithm takes into account several alternative
 possibilities. One is that functionally unrelated genes may have the
 same order due simply because they were adjacent in a common
 ancestor. Other possibilities are that genes may be adjacent in two
 genomes by chance alone, or due to horizontal transfer of the gene
 pair.
 .
 The method is modified from the one described in: Maria D. Ermolaeva,
 Owen White and Steven L. Salzberg. Prediction of Operons in Microbial
 Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
 .
 OperonDB was supported by the NIH under grant R01-LM007938 and by the
 NSF under grant DBI-0234704.
Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/);
 no info about license or downloadable code found, but tried to
 contact authors.

Depends: trnascan-se
Homepage: http://lowelab.ucsc.edu/tRNAscan-SE/
License: GPL
Pkg-URL: http://bioweb.ucr.edu/debian-local/pool/main/t/trnascan-se/
X-Category: tRNA discovery
Pkg-Description: program for improved detection of transfer RNA genes in genomic sequence
 tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence
 while giving less than one false positive per 15 gigabases. Two
 previously described tRNA detection programs are used as fast,
 first-pass prefilters to identify candidate tRNAs, which are then
 analyzed by a highly selective tRNA covariance model. This work
 represents a practical application of RNA covariance models, which
 are general, probabilistic secondary structure profiles based on
 stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000
 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA
 homologues such as selenocysteine tRNAs, tRNA-derived repetitive
 elements and tRNA pseudogenes.

Depends: artemis
Homepage: http://www.sanger.ac.uk/Software/Artemis/
License: GPL 2+
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: genome viewer and annotation tool
 Artemis is a free genome viewer and annotation tool that allows visualization
 of sequence features and the results of analyses within the context of the
 sequence, and its six-frame translation. Artemis is written in Java, and is
 available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK
 database entries or sequence in FASTA or raw format. Extra sequence features
 can be in EMBL, GENBANK or GFF format.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: 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/
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-Description: DNA Sequence Comparison Viewer
 ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer
 based on Artemis. In common with Artemis, ACT is written in Java and
 runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can
 read complete EMBL and GENBANK entries or sequence in FASTA or raw
 format. Extra sequence features can be in EMBL, GENBANK or GFF
 format.
 .
 The sequence comparison displayed by ACT is usually the result of
 running a blastn or tblastx search. See the user manual for more
 information.
 .
 To see ACT in action go to the examples page
 http://www.sanger.ac.uk/Software/ACT/Examples/
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Comment: If you stumble upon alfresco at
 http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and
 tarball vanished from the downlowad page.  So this is not for us even
 if it is linked from Sanger Institute web site.

Comment: If you stumble upon angler at
 http://www.sanger.ac.uk/Software/Angler/ - it seems outdated because
 it is not updated since 1997.  I found no license statement and so
 this is probably also not for us except somebody has real interest
 and volunteers to clarify the license.

Depends: cdna-db
Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/
License: Artistic
Pkg-Description: quality-control checking of finished cDNA clone sequences
 cdna_db is a software system designed for quality-control checking of
 finished cDNA clone sequences, and their computational analysis. The
 combination of a relational db (MySQL) schema, and an
 object-orientated perl API make it easy to implement high-level
 analyses of these transcript sequences.
 .
 The cdna_db can store cDNA clone sequences, and ESTs and
 consensus/contig sequences also derived from these clones. These are
 then used by the system to check cDNA clone sequence identity etc
 (see deneral_doc.txt). For each clone multiple DNA sequence versions
 can be stored, if for instance, the finished DNA sequence is revised
 as part of the sequencing process.
 .
 A blast pipeline is implemented together with a job control system
 (with LSF underlying) so that multiple CPUs can be used in parallel
 to carry out the blasts of large datasets. The searches can be made
 incremental, so as more cDNA sequences are added to the databank,
 just the new clones are blasted.
 .
 Utility scripts are provided to delete previous search results, and
 dump cDNA clones sequences (such as those that passed the QC
 checking) from the cdna_db.

Depends: das-proserver
Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/
License: Same as Perl
Pkg-Description: lightweight Distributed Annotation System (DAS) server
 The Distributed Annotation System (DAS) is a data exchange protocol
 for open sharing of biological information.
 .
 ProServer is a very lightweight DAS server written in Perl. It is
 simple to install and configure and has existing adaptors for a wide
 variety of data sources. It is also easily extensible allowing
 adaptors to be written for other data sources. More information about
 the DAS protocol and what it is useful for is available over at
 http://biodas.org.
 .
 New large scale techniques in biology are producing a rapidly growing
 amount of public available data. Centralized database resources are
 confronted with the task how to scale their storage facilities, how
 to manage frequent updates and how to exchange the data with the
 community.
 .
 The Distributed Annotation System (DAS) addresses these issues. It is
 frequently being used to openly exchange biological annotations
 between distributed sites. Data distribution, performed by DAS
 servers, is separated from visualization, which is done by DAS
 clients.
 .
 DAS is a client-server system in which a client like Ensembl
 integrates information from multiple servers. It allows a single
 machine to gather up genome annotation information from multiple
 distant web sites, collate the information, and display it to the
 user in a single view. Little coordination is needed among the
 various information providers.
 .
 DAS is heavily used in the genome bioinformatics community. Over the
 last years we have also seen growing acceptance in the protein
 sequence and structure communities.

Depends: spice
Homepage: http://www.efamily.org.uk/software/dasclients/spice/
License: GPL
Pkg-Description: Distributed Annotation System (DAS) client
 The Distributed Annotation System (DAS) is a data exchange protocol
 for open sharing of biological information.
 .
 SPICE is a browser for protein sequences, structures and their
 annotations. It can display annotations for PDB, UniProt and Ensembl
 Peptides. All data is retrieved from different sites on the Internet,
 that make their annotations available using the DAS protocol. It is
 possible to add new annotations to SPICE, and to compare them with
 the already available information.

Depends: decipher
Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/
License: To be clarified
Pkg-Description: tracks duplications and deletions of DNA in patients
 DECIPHER tracks submicroscopic duplications and deletions of DNA in
 patients together with phenotypes exhibited by those
 patients. DECIPHER tallies these genetic abnormalities with genes and
 other features of interest in the affected areas. The aim of DECIPHER
 is to provide a research tool to aid clinical diagnosis and treatment
 of these conditions. DECIPHER makes use of DAS technology to
 integrate with Ensembl, the world's leading genome browser.

Depends: est-db
Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/
License: Artistic
Pkg-Description: Software suite for expressed sequence tag (EST) sequencing
 The est_db package is a software suite and database system designed
 to support expressed sequence tag (EST) sequencing projects, and to
 provide comprehensive bioinformatic analysis of sequenced EST
 libraries, for gene discovery and other purposes. The database can
 hold and efficiently process hundreds of thousands of EST sequences,
 track the cDNA libraries and clones to which they belong, and store
 the results of their analysis. Should they be available, large
 compute farms can be used for the analysis.
 .
 Extensive bioinformatic analysis can be carried out on the sequenced
 EST libraries, including similarity (BLAST) searches, protein
 sequence prediction, and the import of EST clustering and assembly
 data from external sources. Results are searchable via a web page,
 with graphic output of the various analyses, enabling one to retrieve
 information pertaining to a particular cDNA clone, or EST read, as
 well as view EST clustering results, or graphical representations of
 BLAST results on the searched EST sequences.
 .
 The est_db package is likely to appeal not only to sequencing groups
 directly employed in EST sequencing, but also to groups interested in
 performing bespoke analysis of ESTs that may already be publically
 available, in order to support their ongoing research aims. The
 package is easily-extensible, via an API designed specifically to
 handle ESTs and their analysis. It is open source and is made
 available free of charge, and, where possible, similarly
 open-licensed components have been used in its development.

Depends: finex
Homepage: http://www.sanger.ac.uk/Software/analysis/finex/
License: To be clarified
Pkg-Description: sequence homology searching
 The FINEX program allows sequence homology searching techniques to be
 applied, where the sequence data is replaced with a fingerprint
 abstracted from the intron/exon boundary phase and the exon length.
 .
 Please note FINEX is no longer supported but is available for
 download.

Depends: hexamer
Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/
License: GPL
Pkg-Description: scan DNA sequences to look for likely coding regions
 Hexamer is a program to scan DNA sequences to look for likely coding
 regions. The principle is to use 6mers, but to avoid deriving any
 information from base composition. Therefore, the frequencies of each
 6mer are normalized by dividing by the total frequency of all 6mers
 with the same base composition.
 .
 There are two programs involved in this process:
  * hextable
    hextable makes files of statistics that hexamer uses to scan for
    likely coding regions.
    The input of hextable is a fasta file of coding sequences in
    frame.  The -o file output is an ascii list of 4096 floating point
    numbers giving log likelihood ratio scores in bits.  The output on
    stdout is a summary of the information content of the table,
    indicating how disriminative it is likely to be.
  * hexamer
    Uses the .hex file from hextable to scan a DNA sequence for likely
    coding regions.
    The input is a fasta DNA file (n.b. that these programs assume all
    'a','c','g','t'. 'n's found in the sequence files will be
    converted to 'c'.
    The output of hexamer is in General Feature Format (GFF) format.

Depends: coot

Depends: r-cran-ape

Depends: caftools
Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
License: Free for non-commercial purposes
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Tools to maintain DNA sequence assemblies
 This is V2 of the CAF (Common Assembly Format) C-tools.  It comprises
 a set of libraries and programs for manipulating DNA sequence
 assemblies using CAF files.
 .
 The CAF specification can be found at:
 http://www.sanger.ac.uk/Software/formats/CAF/
Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
 maintains a package called bio-linux-assembly-conversion-tools which
 contains caftools and roche2gap in one package with the following
 description:
 .
 Conversion tools for handling 454 assemblies.
 .
 This package contains code from different authors that allow sequence
 assemblies to be converted into formats such as CAF (Common Assembly
 Format) or GAP4. This package includes tools to convert assemblies
 from Newbler's ace format for loading into a gap4 assembly.

Depends: roche454ace2caf
Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
License: not specified
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: convert GS20 or FLX assemblies into CAF format
 Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into
 CAF format so that these are correct viewable/editable/... whithin
 the staden package (gap4).  You have then access to "hidden data",
 exact aligned trace and there positions, base values etc and whith
 staden-1-7-0 you have graphical access to the associated flowgramm
 traces (SFF format).
 .
 Description, Goals - please take a look at
 http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf
Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
 maintains a package called bio-linux-assembly-conversion-tools which
 contains caftools and roche2gap in one package with the following
 description:
 .
 Conversion tools for handling 454 assemblies.
 .
 This package contains code from different authors that allow sequence
 assemblies to be converted into formats such as CAF (Common Assembly
 Format) or GAP4. This package includes tools to convert assemblies
 from Newbler's ace format for loading into a gap4 assembly.

Depends: big-blast
Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl
License: not specified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Helper tool to run blast on large sequences
 This script will chop up a large sequence, run blast on each bit and
 then write out an EMBL feature table and a MSPcrunch -d file
 containing the hits.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: blixem
Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html
License: not specified
Responsible: BioLinux - Dan Swan <dswan@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: interactive browser of pairwise Blast matches
 Blixem (BLast matches In an X-windows Embedded Multiple alignment),
 is an interactive browser of pairwise Blast matches that have been
 stacked up in a ma ster-slave multiple alignment
Remark: The link to the source archive on the web pages is not valid any more - it might be a problem to obtain the source.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: 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@ceh.ac.uk>
X-Category: Sequence assembly
X-Importance: not a lot of alternatives
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: DNA Sequence Assembly Program
 CAP3 contains the following improvements to the CAP sequence assembly
 program.
  1. Use of forward-reverse constraints to correct assembly errors and
     link contigs.
  2. Use of base quality values in alignment of sequence reads.
  3. Automatic clipping of 5' and 3' poor regions of reads.
  4. Generation of assembly results in ace file format for Consed.
  5. CAP3 can be used in GAP4 of the Staden package.
 These improvements allow CAP3 to take longer sequences of higher
 errors and produce more accurate consensus sequences.
Remark: Obtaining the source requires to fill in a registration form
 Official distribution in Debian is probably impossible.  The
 package included in the BioLinux distribution
 http://envgen.nox.ac.uk/biolinux.html containins only the binaries
 cap3 and formcon, dated Aug 29, 2002.  This package exists purely for
 convenience to Bio-Linux users so that the files are placed in
 locations consistent with the Bio-Linux setup.

Comment: BioLinux contains a clcworkbench package which is available
 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
Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html
License: not specified
Responsible: BioLinux - Nathan S Haigh <n.haigh@sheffield.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: outdated program to estimate population-genetic parameters
 COALESCE fits the model which has a single population of constant
 size, and estimates 4Nu, where N is the effective population size and
 u is the neutral mutation rate per site. You may also want the
 Postscript or the TeX file of the preprint version of the Kuhner,
 Yamato, and Felsenstein 1995 paper.
Remark: This software is probably outdated
 The homepage contains the explicite link: "We are no longer
 supporting COALESCE as its functions can be done just as well by
 LAMARC and it's easier for us to support just one program. You may
 still want the paper, however."  So this is actually no target for
 the Debian Med distribution but just a hint for users about the
 existence of this program and the even better alternative even if
 BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
 a package.

Comment: BioLinux contains a dendroscope package which is available
 at http://www.dendroscope.org but this project has only a
 "free as in beer" binary download - so this is not for us ...

Depends: estferret
Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm
License: to be clarified
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: processes, clusters and annotates EST data
 ESTFerret processes, clusters and annotates EST data. It is
 user-configurable. Results are currently stored in a series of text
 tables. Annotation consists of searches against use r-defined blast
 databases, prosite, GO and allocation of EC numbers where possible.
 .
 EST-ferret is a user-configurable, automated pipeline for the
 convenient analysis of EST sequence data that includes all of the
 necessary steps for cleanup and trimming, submission to external
 sequence repositories, clustering, identification by BLAST homology
 searches and by searches of protein domain databases, annotation with
 computer-addressable terms and production of outputs for direct entry
 into microarray analysis packages. It is composed of several widely
 used, open-source algorithms, including PHRED, CAP3, BLAST, and a
 range of sequence and annotation databases, including Gene Ontology
 and Conserved Domain Database to deliver a putative identity and a
 detailed annotation of each clone. It can be run either step-by-step
 to track the outputs, or as a single batch process. Users can easily
 edit the configuration file to define parameter settings.
 .
 This package has five major components: (1) ESTs coding system; (2)
 sequence processing; (3) sequence clustering; (4) sequence annotating
 and (5) storage and reporting of results. DNA trace files are renamed
 and converted into FASTA format, cleaned and submitted to
 dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of
 CAP3 to assemble the ESTs into groups corresponding to separate gene
 families and unique genes. Sequence identification and annotation is
 provided by a series of BLAST homology searches (Parallel_BLAST and
 Priority_BLAST) against user-defined sequence databases implemented
 with the NCBI BLASTALL algorithm. The BLAST results are parsed and
 annotation terms that reflect functional attributes are captured from
 Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme
 Commission (EC) databases and applied to each of the clones. CDD (and
 InterPro) searches are performed for seeking protein domains in the
 sequences. Other options are provided to run PatSearch, RepeatMasker
 and BLAT to find UTRs, repeats and EST candidates in
 genomes. Finally, the package generates analysis reports in a variety
 of flat file formats, sources of which can be serve as inputs for
 some gene annotation and gene expression profiling tools, and also as
 a MySQL database or web-browsable search tool.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: estscan
Homepage: http://estscan.sourceforge.net/
License: free
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: detect coding regions in DNA sequences, even if of low quality
 ESTScan is a program that can detect coding regions in DNA sequences,
 even if they are of low quality. It will also detect and correct
 sequencing errors that lead to fr ameshifts.
 .
 ESTScan is not a gene prediction program, nor is it an open reading
 frame detector. In fact, its strength lies in the fact that it does
 not require an open reading frame to detect a coding region. As a
 result, the program may miss a few translated amino acids at either
 the N or the C terminus, but will detect coding regions with high
 selectivity and sensitivity.
 .
 Similarly to GENSCAN, ESTScan uses a Markov model to represent the
 bias in hexanucleotide usage found in coding regions relative to
 non-coding regions. Additionally, ESTScan allows insertions and
 deletions when these improve the coding region statistics. Further
 details can be found at:
 http://www.ch.embnet.org/software/ESTScan2_help.html
 .
 References:
  * Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing
    errors by combining Hidden Markov models Bioinformatics 19,
    ii103-ii112.
  * Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for
    detecting, evaluating, and reconstructing potential coding regions in
    EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: fasta
Homepage: http://www.ebi.ac.uk/Tools/fasta/
License: no inclusion into commercial product
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: searching DNA and protein databases
 FASTA (pronounced FAST-AYE) stands for FAST-ALL, reflecting the fact
 that it can be used for a fast protein comparison or a fast
 nucleotide comparison. This program achieves a high level of
 sensitivity for similarity searching at high speed. This is achieved
 by performing optimised searches for local alignments using a
 substitution matrix. The high speed of this program is achieved by
 using the observed pattern of word hits to identify potential matches
 before attempting the more time consuming optimised search. The
 trade-off between speed and sensitivity is controlled by the ktup
 parameter, which specifies the size of the word. Increasing the ktup
 decreases the number of background hits. Not every word hit is
 investigated but instead initially looks for segment's containing
 several nearby hits.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: fluctuate
Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html
License: not specified
Responsible: BioLinux - Nathan S Haigh <n.haigh@sheffield.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: outdated program to model a single population
 FLUCTUATE fits the model which has a single population which has been
 growing (or shrinking) according to an exponential growth law. It
 estimates 4Nu and g, where N is the effective population size, u is
 the neutral mutation rate per site, and g is the growth rate of the
 population.
Remark: This software is probably outdated
 The homepage contains the explicite link: "We are no longer
 supporting FLUCTUATE as its functions can be done just as well by
 LAMARC and it's easier for us to support just one program. You may
 still want the paper, however."  So this is actually no target for
 the Debian Med distribution but just a hint for users about the
 existence of this program and the even better alternative even if
 BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
 a package.

Depends: lamarc
Homepage: http://evolution.gs.washington.edu/lamarc/
License: Apache V2.0
Responsible: BioLinux - Nathan S Haigh <n.haigh@sheffield.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: estimate population-genetic parameters
 LAMARC is a program which estimates population-genetic parameters
 such as population size, population growth rate, recombination rate,
 and migration rates. It approximates a summation over all possible
 genealogies that could explain the observed sample, which may be
 sequence, SNP, microsatellite, or electrophoretic data. LAMARC and
 its sister program Migrate are successor programs to the older
 programs Coalesce, Fluctuate, and Recombine, which are no longer
 being supported. The programs are memory-intensive but can run
 effectively on workstations.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: lucy
Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html
License: GPL
Responsible: BioLinux - Dan Swan <dswan@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: DNA sequence quality and vector trimming tool
 Lucy is a utility that prepares raw DNA sequence fragments for
 sequence assembly, possibly using the TIGR Assembler. The cleanup
 process includes quality assessment, confidence reassurance, vector
 trimming and vector removal. The primary advantage of Lucy over other
 similar utilities is that it is a fully integrated, stand alone
 program.
 .
 Lucy was designed and written at The Institute for Genomic Research
 (TIGR, now the J. Craig Venter Institute), and it has been used here
 for several years to clean sequence data from automated DNA
 sequencers prior to sequence assembly and other downstream uses.  The
 quality trimming portion of lucy makes use of phred quality scores,
 such as those produced by many automated sequencers based on the
 Sanger sequencing method.  As such, lucy’s quality trimming may not
 be appropriate for sequence data produced by some of the new
 “next-generation” sequencers.
 .
 See also the SourceForge page at http://lucy.sourceforge.net/.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: maxd
Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/
License: Artistic
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: data warehouse and visualisation environment for genomic expression data
 Maxd is a data warehouse and visualisation environment for genomic
 expression data. It is being developed in the University of
 Manchester by the Microarray Bioinformatics Group.
 .
 Software components:
  maxdLoad2 - standards-compliant, highly customisable transcriptomics
              database
  maxdView  - modular and easily extensible data visualisation and
              analysis environment
  maxdSetup - installation management utility
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: mesquite
Homepage: http://mesquiteproject.org/mesquite/mesquite.html
License: LGPL
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: help biologists analyze comparative data about organisms
 Mesquite is software for evolutionary biology, designed to help
 biologists analyze comparative data about organisms. Its emphasis is
 on phylogenetic analysis, but some of its modules concern population
 genetics, while others do non-phylogenetic multivariate
 analysis. Because it is modular, the analyses available depend on the
 modules installed. Analyses include:
  * Reconstruction of ancestral states (parsimony, likelihood)
  * Tests of process of character evolution, including correlation
  * Analysis of speciation and extinction rates
  * Simulation of character evolution (categorical, DNA, continuous)
  * Parametric bootstrapping (integration with programs such as PAUP*
    and NONA)
  * Morphometrics (PCA, CVA, geometric morphometrics)
  * Coalescence (simulations, other calculations)
  * Tree comparisons and simulations (tree similarity, Markov
    speciation models)
 There is a brief outline of features, which includes
 screenshots. Mesquite is not primarily designed to infer phylogenetic
 trees, but rather for diverse analyses using already inferred trees.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: migrate
Homepage: http://popgen.scs.fsu.edu/Migrate-n.html
License: to be clarified
Responsible: BioLinux - Nathan S Haigh <n.haigh@sheffield.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: estimation of population sizes and gene flow using the coalescent
 Migrate estimates effective population sizes and past migration rates
 between n population assuming a migration matrix model with
 asymmetric migration rates and different subpopulation sizes. Migrate
 uses maximum likelihood or Bayesian inference to jointly estimate all
 parameters. It can use the followind data types: sequence data using
 Felsenstein's 84 model with or without site rate variation, single
 nucleotide polymorphism data, microsatellite data using a stepwise
 mutation model or a brownian motion mutation model, and
 electrophoretic data using an 'infinite' allele model. The output can
 contain: Estimates of all migration rates and all population sizes,
 assuming constant mutation rates among loci or a gamma distributed
 mutation rate among loci. Profile likelihood tables, Percentiles,
 Likelihood-ratio tests, and simple plots of the log-likelihood
 surfaces for all populations and all loci.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: msatfinder
Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
License: GPL
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: identification and characterization of microsatellites in a comparative genomic context
 Msatfinder is a Perl script designed to allow the identification and
 characterization of microsatellites in a comparative genomic
 context. There is also an online manual, a discussion forum and an
 online interface where users can do searches in any number of DNA or
 protein sequences (as long as the maximum size of all sequences does
 not exceed 10MB). Nucleotide and amino acid sequences in GenBank,
 FASTA, EMBL and Swissprot formats are supported.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: mview
Homepage: http://bio-mview.sourceforge.net/
License: GPL
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: reformat results of a sequence database search or a multiple alignment
 MView is a tool for converting the results of a sequence database
 search (BLAST, FASTA, etc.) into the form of a coloured multiple
 alignment of hits stacked against the query. Alternatively, an
 existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be pr
 ocessed.  It reformats the results of a sequence database search or a
 multiple alignment adding optional HTML markup to control colouring
 and web page layout. MView is not a multiple alignment program, nor
 is it a general purpose alignment editor.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: oligoarrayaux
Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php
License: non-free (fre academical use)
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Prediction of Melting Profiles for Nucleic Acids
 OligoArrayAux is a subset of the UNAFold package for use with
 OligoArray (http://berry.engin.umich.edu/oligoarray2_1/). OligoArray
 is a free software that computes gene specific oligonucleotides for
 genome-scale oligonucleotide microarray construction.  (It is not
 really specified what they mean with "free software". You can
 download the source code after registration: "registration is the
 only way for me to keep trace of OligoArray users and be able to send
 you a bug fix or a new release".)
 .
 The original UNAFold server is available at
 http://dinamelt.bioinfo.rpi.edu/download.php and you should probably
 read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about
 "Prediction of Melting Profiles for Nucleic Acids".
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 Finally it is hard to find some documentation what OligoArrayAux is
 really doing because it is only specified into relation to OligoArray
 (as precondition) and UNAFold (as subset of this) but BioLinux
 distribution http://envgen.nox.ac.uk/biolinux.html decided to package
 this and so it might make soem sense to list it here - further
 investigation is needed.

Depends: omegamap
Homepage: http://www.danielwilson.me.uk/software.html
License: to be clarified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: detecting natural selection and recombination in DNA or RNA sequences
 OmegaMap is a program for detecting natural selection and
 recombination in DNA or RNA sequences. It is based on a model of
 population genetics and molecular evolution. The signature of natural
 selection is detected using the dN/dS ratio (which measures the
 relative excess of non-synonymous to synonymous polymorphism) and the
 signature of recombination is detected from the patterns of linkage
 disequilibrium. The model and the method of estimation are described
 in
  Wilson, D. J. and G. McVean (2006)
  Estimating diversifying selection and functional constraint in the
  presence of recombination.
  Genetics doi:10.1534/genetics.105.044917.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: partigene
Homepage: http://www.nematodes.org/bioinformatics/PartiGene/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: generating partial gemomes
 PartiGene is part of the Edinburgh-EGTDC developed EST-software
 pipeline at the moment consisting of trace2dbEST, PartiGene,
 wwwPartiGene, port4EST and annot8r. PartiGene is a menu-driven,
 multi-step software tool which takes sequences (usually ESTs) and
 creates a dataabase of a non-redundant set of sequence objects
 (putative genes) which we term a partial genome.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: pfaat
Homepage: http://pfaat.sourceforge.net/
License: GPL
Responsible: BioLinux - Dan Swan <dswan@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Protein Family Alignment Annotation Tool
 Pfaat is a Java application that allows one to edit, analyze, and
 annotate multiple sequence alignments. The annotation features are a
 key component as they provide a framework to for further sequence,
 structure and statistical analysis.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Comment: priam
 BioLinux contains a priam package which is available at
 http://bioinfo.genotoul.fr/priam/REL_JUL06/index_jul06.html but this
 project has only a "free as in beer" binary download - so this is not
 for us ...

Depends: prot4est
Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: EST protein translation suite
 prot4EST is a perl script that takes expressed sequence tags (ESTs)
 and translates them optimally to produce putative peptides. prot4EST
 intergrates a number of programs to overcome problems inherent with
 translating ESTs.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: qtlcart
Homepage: http://statgen.ncsu.edu/qtlcart/
License: GPL
Responsible: BioLinux - Dan Swan <dswan@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: map quantitative traits using a map of molecular markers
 QTL Cartographer is a suite of programs to map quantitative traits
 using a map of molecular markers. It contains a set of programs that
 will aid in locating the genes that control quantitative traits using
 a molecular map of markers.  It includes some programs to allow
 simulation studies of experiments.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: rbs-finder
Homepage: http://www.genomics.jhu.edu/RBSfinder/
License: not specified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: find ribosome binding sites(RBS)
 The program implements an algorithm to find ribosome binding
 sites(RBS) in the upstream regions of the genes annotated by
 Glimmer2, GeneMark, or other prokaryotic gene finders.  If there is
 no RBS-like patterns in this region, program searches for a start
 codon having a RBS-like pattern ,in the same reading frame upstream
 or downstream and relocates start codon accordingly.
 .
 You can find more detailed information at
 http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: recombine
Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
License: not specified
Responsible: BioLinux - Nathan S Haigh <n.haigh@sheffield.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: effective population size of populations
 RECOMBINE fits a model which has a single population of constant size
 with a single recombination rate across all sites. It can accomodate
 either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism)
 data. It estimates 4Nu and r, where N is the effective population
 size, u is the neutral mutation rate per site, and r is the ratio of
 the per-site recombination rate to the per-site mutation rate.
Remark: This software might be outdated
 The homepage contains the explicite link: "We are no longer
 supporting RECOMBINE as its functions can be done just as well by
 LAMARC and it's easier for us to support just one program. You may
 still want the paper, however."  So this is actually no target for
 the Debian Med distribution but just a hint for users about the
 existence of this program and the even better alternative even if
 BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
 a package.

Depends: splitstree
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html
License: to be clarified
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: Analyzing and Visualizing Evolutionary Data
 Evolutionary data is most often presented as a phylogentic tree, the
 underlying assumption being that evolution is a branching
 process. However, real data is never ideal and thus doesn't always
 support a unique tree, but often supports more than one possible
 tree. Hence, it makes sense to consider tree reconstruction methods
 that produce a tree, if the given data heavily favors one tree over
 all others, but otherwise produces a more general graph that
 indicates different possible phylogenies. One such method is the
 Split Decomposition introduced by Hans-Juergen Bandelt and Andreas
 Dress (1992) and its variations. Another example is Spectral Analysis
 developed by Hendy, Penny and others.
 .
 These and other methods are implemented in the program SplitsTree,
 that I wrote with contributions from Dave Bryant, Mike Hendy, Holger
 Paschke, Dave Penny and Udo Toenges. It is based on the Nexus
 format.
 .
 Note: There is a new version 4.0 written from scratch at
 http://www.splitstree.org/ which requires a license key - so this is
 probably non-free.  Version 3.2 which is linked above has some
 downloadable source code without any license or copyright statement -
 so it has to be clarified whether we are able to distribute this code
 or not.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html


Depends: taverna
Homepage: http://taverna.sourceforge.net/
License: LGPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: designing and executing myGrid workflows for bioinformatics
 The Taverna workbench is a free software tool for designing and
 executing workflows, created by the myGrid  project, and funded
 through OMII-UK. Taverna allows users to integrate many different
 software tools, including web services, such as those provided by the
 National Center for Biotechnology Information, The European
 Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab,
 BioMOBY and EMBOSS.
 .
 The Taverna Workbench provides a desktop authoring environment and
 enactment engine for scientific workflows expressed in Scufl (Simple
 Conceptual Unified Flow language). The Taverna enactment engine is
 also available separately, and other Scufl enactors are available
 including Moteur. The myExperiment social web site supports finding
 and sharing of workflows and has special support for Scufl
 workflows. The Taverna workbench, myExperiment and associated
 components are developed and maintained by the myGrid team, in
 collaboration with the open source community.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: taxinspector
Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html
License: Artistic + other free licenses
Responsible: BioLinux - Tim Booth <tbooth@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: browser for entries in the NCBI taxonomy
 TaxInspector is a browser for entries in the NCBI taxonomy. It is
 designed to run as a plugin to annotation software such as maxdLoad2
 and Pedro, but also has a standalone mode.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: tetra
Homepage: http://www.megx.net/tetra/
License: free academic
Responsible: BioLinux - Stewart Houten <shou@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: tetranucleotide frequency calculator
 The TETRA program can be used to calculate how well tetranucleotide
 usage patterns in DNA sequences correlate. Such correlations can
 provide valuable hints on the relatedne ss of DNA sequences, and are
 particularly useful for metagenomic sequences.
Remark: for the Linux version
 Version 1.0.2 (Mac OSX has version
 2.0b30) is deprecated and hence a feature-limited version of
 TETRA. At the time writing, no decisions have been made about
 adapting and cross-compiling the Mac OS X code for this platform. A
 Linux version might happen when REALbasic's Linux IDE is more mature.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: trace2dbest
Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/
License: GPL
Responsible: BioLinux - Bela Tiwari <btiwari@ceh.ac.uk>
Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Pkg-Description: process trace files into dbEST submissions
 Trace2dbest is part of the PartiGene pipeline.
 .
 Trace2dbest takes a series of sequence traces and converts them into
 basecalled files. It also creates files in the appropriate format for
 submission to dbEST and allows you to submit them directly if your
 machine is configured to allow mailing to external sites.  The output
 from trace2dbest can be used as input to the PartiGene program.
 .
 Trace2dbEST process raw sequenceing chromatograph trace files from
 EST projects into quality-checked sequences, ready for submission to
 dbEST. trace2dbEST guides you through the creation of all the
 necessary files for submission of ESTs to dbEST. trace2dbest makes
 use of other software (available free under academic licence) that
 you will need to have installed, namely phred, cross_match and
 (optionaly) BLAST.
Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html

Depends: profit
WNPP: 525428
Remark: The authors need to change the license, still.

Depends: obo-edit
Homepage: http://www.geneontology.org
X-Comment: Find the license here [1] and [2].
 [1] http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/tags/2.2/release_resources/LICENSE?revision=4863&view=markup
 [2] http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/tags/2.2/release_resources/ARTISTIC_LICENSE?revision=4863&view=markup
License: Artistic
Pkg-Description: editor for biological ontologies
 (Open Biological Ontologies) Obo-Edit supports the formal representation
 of biological entities and the specification of is-a (specialisation)
 and part-of relations. Amongst the databases cureated by this tool
 is the GeneOntology.


Depends: jstreeview
Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml
License: MIT/X11
Language: JavaScript
Pkg-Description: Editor for Phylogenetic Trees
 A concise viewer/editor for phylogenetic trees in the Newick format.
 The core functions are written in JavaScript, using the canvas tag
 proposed by HTML 5. No server side support is needed for rendering the
 picture and therefore you can grab this page together with knhx.js and
 canvastext.js to locally view your trees in a supported web browser.
 .
 The source can be downloaded at
 http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip

Depends: phagefinder
Homepage: http://phage-finder.sourceforge.net/
License: GPL
Language: Perl
X-Category: Genomics; Prophage detection in prokaryotes
Pkg-Description: heuristic computer program to identify prophage regions within bacterial genomes
 It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a
 collection of bacteriophage protein sequences and results from HMMSEARCH analysis of
 441 phage-specific HMMs to locate prophage regions. By using FASTA33, MUMMER  or BLASTN,
 it can find potential attachment (att) sites of the phage region(s). Data from tRNAscan-SE
 and Aragorn  are used to determine whether a tRNA  or tmRNA  served as the putative target
 for integration. Additionally, by looking for the presence or absence of specific proteins
 using specific HMM models, Phage_Finder can predict whether the region is most likely
 prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a
 degenerate phage region.
 .
 The goal of this project is to provide an open-sourced, standardized and automated system
 to identify and classify prophages within prokaryotic genomes. It is hoped that this package
 will facilitate future studies on the biology and evolution of these prophages by providing
 a level of microbial genome annotation that was previously void.

Depends: codonw
Homepage: http://codonw.sourceforge.net/
License: GPL
X-Category: Genomics; Codon usage analysis
Pkg-Description: Correspondence Analysis of Codon Usage
 CodonW is a programme designed to simplify the Multivariate analysis (correspondence
 analysis) of codon and amino acid usage. It also calculates standard indices of codon
 usage. It has both menu and command-line interfaces. It was written by John Peden in
 the lab of Paul Sharp,  Dept of Genetics,  University of Nottingham. John is working
 in human genetics and is currently employed as ProCardis database manager at the WTCHG
 in Oxford University.

Depends: compclust
Homepage: http://woldlab.caltech.edu/compclust/
License: MLX (http://woldlab.caltech.edu/compclust/LICENSE.txt)
Language: Python
X-Category: Genomics; Clustering analysis (+GUI)
Pkg-URL: http://woldlab.caltech.edu/compclust/debian_install.shtml
Pkg-Description: explore and quantify relationships between clustering results
 CompClust is a python package written using the pyMLX and IPlot APIs. It provides
 software tools to explore and quantify relationships between clustering results. Its
 development has been largely built around needs of microarray data analysis but could
 be easily used in other domains.
 .
 Briefly pyMLX provides for efficient and convenient execution of many clustering
 algorithms using a extendable library of algorithms. It also provides many-to-many
 linkages between data features and annotations (such as cluster labels, gene names,
 gene ontology information, etc.) These linkages persist through varied data
 manipulations. IPlot provides an abstraction of the plotting process in which any
 arbitrary feature or derived feature of the data can be projected onto any feature
 of the plot, including the X,Y coordinates of points, marker symbol, marker size,
 maker/line color, etc. These plots are intrinsically linked to the dataset, the
 View and the Labeling classes found within pyMLX.

Depends: treebuilder3d
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder
License: GPL
Language: Java
X-Category: Clustering; SAGE expression
Pkg-Description: viewer of SAGE and other types of gene expression data
 TreeBuilder3D is an interactive viewer that allows organization of SAGE and other
 types of gene expression data such as microarrays into hierarchical dendrograms,
 or phenetic networks (the term 'phenetic' used as the analysis relies on principals,
 used in phylogenetic analysis by system biology). Might be used as a visual aid when
 analyzing differences in expression profiles of SAGE libraries, serves as an
 alternative to Venn diagrams.

Depends: excavator
Homepage: http://csbl.bmb.uga.edu/downloads/excavator/
License: GPL
Language: Java
X-Category: Clustering; Gene expression data
Pkg-Description: gene expression data clustering
 Excavator is a program for gene expression data clustering. It uses a set of unique
 clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at
 the University of Georgia. Excavator represents data internally as a minimum spanning
 tree and outputs results to the user through the use of a micro-array data window,
 graphs, and a dendrogram viewer.
 .
 Features
  * partitioning gene expressions profiles using multiple methods of clustering and
    definitions of distance between profiles.
  * automatic selection of the most plausible number of clusters in a data set
  * three different ways of viewing data: Micro-array, Gene Expression, and Dendrogram.
    As well as graphing individual genes from each cluster independently.
  * identification of genes with expression profiles similar to specified seed genes
  * cluster identification from a noisy background
  * numerical comparison between different clustering results of the same data set
  * runnable on command line as well as through a Java GUI

Depends: tigr-assembler
Homepage: http://www.jcvi.org/cms/research/software/
License: free (OSI-certified)
X-Category: Assembling
Pkg-Description: whole-genome assembly
 Enabled the first published whole-genome assembly of a free-living organism in 1995.
 Last revised in 2003.
 .
 See also http://www.jcvi.org/cms/publications/listing/abstract/article/tigr-assembler-a-new-tool-for-assembling-large-shotgun-sequencing-projects/
Remark: It seems that wgs-assembler is the more up to date program.  Moreover there
 seems to be no download option for TIGR Assembler at the J. Craig Venter Institute
 (formerly TIGR) any more.

Depends: treetime
Homepage: http://treetime.linhi.com/
License: GPL
Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data
 TreeTime is controlled by input files in nexus format and does
 bayesian sampling of phylogenetic trees from these data.

Depends: abacas

Depends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun

Depends: profphd-net, profphd-utils

Depends: profphd

Depends: abyss

Depends: ampliconnoise

Depends: disulfinder

Depends: circos

Depends: populations

Depends: raccoon

Depends: librg-utils-perl

Depends: snap

Depends: vcftools

Suggests: mobyle, mobyle-programs, mobyle-tutorials

Depends: hilbertvisgui
Homepage: http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/HilbertVisGUI.html
License: GPL-3
Pkg-Description: interactive tool to visualize long vectors of integer data by means of Hilbert curves
 An interactive tool to visualize long vectors of integer data by means of Hilbert
 curves.  It provides a GUI for the Debian packaged r-bioc-hilbertvis and is thus
 interesting for giving users some comfort.  Until this software is not yet packaged
 you can follow the hint at the homepage how to use it with R.

Depends: beads
Homepage: http://pappso.inra.fr/bioinfo/beads
License: CeCILL
Pkg-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages
Pkg-Description: 2-DE electrophoresis gel image spot detection
 BEADS is a program for spot detection on 2-D gel images. It is based on
 an analogy with beads flowing uphill on the surface of the gel image and
 on the analysis of their paths

Depends: x-tandem-pipeline
Homepage: http://pappso.inra.fr/bioinfo/xtandempipeline/
License: GPL
Language: Java
Pkg-Description: peptide/protein identification from MS/MS mass spectra
 X!Tandem is an open-source software performing peptide/protein
 identification from MS/MS mass spectra. X!Tandem is fast and accurate,
 but the Global Proteome Machine (GPM) is relatively limited regarding
 the processing of identification results. X!Tandem pipeline is an
 alternative to the installation of the GPM on local servers.  X!Tandem
 pipeline performs database searching and matching on a list of MS/MS
 runs in one shot, using a list of easily user selected paramaters and
 databases.  X!Tandem pipeline also performs filtering of data according
 to statistical values at peptide and protein levels. The results are
 stored into TSV (Tab Separated Values) files. Moreover, redundancy of
 protein databases are fully filtered as follows :
  * proteins identified without specific peptides compared to others are
    eliminated;
  * proteins identified with the same pool of peptides are assembled;
  * proteins are grouped by function (identified with at least one common
    peptide), and the specific peptides for each sub-group of proteins are
    indicated.

Suggests: maude

Depends: forge
Homepage: http://combiol.org/forge/
License: Apache 2.0
Pkg-Description: genome assembler for mixed read types
 Forge Genome Assembler is a parallel, MPI based genome assembler for
 mixed read types.
 .
 Forge is a classic "Overlap layout consensus" genome assembler written
 by Darren Platt and Dirk Evers. Implemented in C++ and using the
 parallel MPI library, it runs on one or more machines in a network and
 can scale to very large numbers of reads provided there is enough
 collective memory on the machines used. It generates a full consensus
 alignment of all reads, can handle mixtures of sanger, 454 and illumina
 reads. There is some support for solid color space and it includes built
 in tools for vector trimming and contamination screening.
 .
 Forge and was originally developed at Exelixis and they have kindly
 agreed to place the software which underwent much subsequent development
 outside Exelixis, into the public domain. Forge works with most of the
 common MPI implementations.
Remark: Competitor to MIRA2 and wgs-assembler
 This package was requested by William Spooner <whs@eaglegenomics.com> as
 a competitor to MIRA2 and wgs-assembler.

Depends: metarep
License: MIT
Homepage: http://www.jcvi.org/metarep/
Pkg-Description: JCVI Metagenomics Reports
 JCVI Metagenomics Reports (METAREP) is a new open source tool for
 high-performance comparative metagenomics. It provides a suite of web
 based tools to help scientists to view, query, browse and compare
 metagenomics annotation data derived from ORFs called on metagenomics
 reads.
 .
 METAREP supports browsing of functional and taxonomic assignments.
 Users can either specify fields, or logical combinations of fields to
 flexibly filter datasets on the fly. Users can compare multiple datasets
 at various functional and taxonomic levels applying statistical tests as
 well as hierarchical clustering, multidimensional scaling and heatmaps.


X-Comment: Not sure whether this can be distributed at all - asking
 might not harm because I've got a serious hint that this software
 is quite interesting
X-Depends: megan
X-License: Registriation required
X-Homepage: http://www-ab.informatik.uni-tuebingen.de/software/megan
X-Pkg-Description: MEtaGenome ANalyzer
 In metagenomics, the aim is to understand the composition and operation
 of complex microbial consortia in environmental samples through
 sequencing and analysis of their DNA. Similarly, metatranscriptomics and
 metaproteomics target the RNA and proteins obtained from such samples.
 Technological advances in next-generation sequencing methods are fueling
 a rapid increase in the number and scope of environmental sequencing
 projects. In consequence, there is a dramatic increase in the volume of
 sequence data to be analyzed.

Depends: arachne
Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
License: free
Pkg-Description: toolkit for Whole Genome Shotgun Assembly
 Arachne is a toolkit developed for Whole Genome Shotgun Assembly.
 Arachne consists of a comprehensive set of modules, including a central
 pipeline (Assemblez) that can be run on almost any genome to produce a
 draft assembly. Arachne's mandate explicitly includes accommodating
 difficult genomes with complications such as extreme size, repeats, and
 high polymorphism rates. In order to construct a reasonably
 well-connected assembly from such tricky genomes, Arachne provides
 further tools that can be used after the main module pipeline.
 .
 The Arachne code package has been under continuous development since
 2000. It began with the classic "overlap-layout-consensus" paradigm and
 has since developed into a vast collection of tools, implemented in
 numerous modules, to analyze, visualize and manipulate assemblies. New
 and improved algorithms are becoming available on a regular basis.

Depends: maker2
Homepage: http://www.yandell-lab.org/software/maker.html
License: GPL / Artistic
Pkg-Description: annotate genomes and create genome databases
 MAKER is a portable and easily configurable genome annotation pipeline.
 It's purpose is to allow smaller eukaryotic and prokaryotic genome
 projects to independently annotate their genomes and to create genome
 databases. MAKER identifies repeats, aligns ESTs and proteins to a
 genome, produces ab-initio gene predictions and automatically
 synthesizes these data into gene annotations having evidence-based
 quality values. MAKER is also easily trainable: outputs of preliminary
 runs can be used to automatically retrain its gene prediction algorithm,
 producing higher quality gene-models on seusequent runs. MAKER's inputs
 are minimal and its ouputs can be directly loaded into a GMOD database.
 They can also be viewed in the Apollo genome browser; this feature of
 MAKER provides an easy means to annotate, view and edit individual
 contigs and BACs without the overhead of a database. MAKER should prove
 especially useful for emerging model organism projects with minimal
 bioinformatics expertise and computer resources

Depends: repeatmasker
Homepage: http://www.repeatmasker.org/
License: Open Software License v. 2.1
Pkg-Description: screens DNA sequences for interspersed repeats
 RepeatMasker is a program that screens DNA sequences for interspersed
 repeats and low complexity DNA sequences. The output of the program is a detailed
 annotation of the repeats that are present in the query sequence as well as a
 modified version of the query sequence in which all the annotated repeats have
 been masked (default: replaced by Ns). On average, almost 50% of a human genomic
 DNA sequence currently will be masked by the program. Sequence comparisons in
 RepeatMasker are performed by one of several popular search engines including,
 cross_match, ABBlast/WUBlast, RMBlast and Decypher.

Depends: rmblast
Homepage: http://tandem.bu.edu/trf/trf.html
License: Same as blast2
Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST
 RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST
 suite. The primary difference between this distribution and the NCBI
 distribution is the addition of a new program "rmblastn" for use with
 RepeatMasker and RepeatModeler.
 RMBlast supports RepeatMasker searches by adding a few necessary features
 to the stock NCBI blastn program. These include: Support for custom matrices
 ( without KA-Statistics ). Support for cross_match-like complexity adjusted
 scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm.
 Support for cross_match-like masklevel filtering.

Depends: augustus
Homepage: http://augustus.gobics.de/
License: not explicitely specified
Pkg-Description: predict genes in eukaryotic genomic sequences
 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
 It can be run on this web server or be downloaded and run locally. It is
 open source so you can compile it for your computing platform. You can now
 run AUGUSTUS on the German MediGRID. This enables you to submit larger
 sequence files and allows to use protein homology information in the
 prediction. The MediGRID requires an instant easy registration by email
 for first-time users.

Depends: e-hive
Homepage: http://www.ensembl.org/info/docs/eHive/index.html
License: Not specified
Pkg-Description: distributed processing system based on 'autonomous agents'
 This is a distributed processing system based on 'autonomous agents' and
 Hive behavioural structure of Honey Bees .  It implements all functionality
 of both data-flow graphs and block-branch diagrams which should allow it
 to codify any program, algorithm, or parallel processing job control system.
 It is not bound to any processing 'farm' system and can be adapted to any GRID.

Depends: cmap
Homepage: http://gmod.org/wiki/CMap
License: Not specified
Pkg-Description: view comparisons of genetic and physical maps
 CMap is a web-based tool that allows users to view comparisons of genetic and
 physical maps. The package also includes tools for curating map data.

Depends: gbrowse-syn
Homepage: http://gmod.org/wiki/GBrowse_syn
License: Not specified
Pkg-Description: Generic Synteny Browser
 GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny
 browser designed to display multiple genomes, with a central reference
 species compared to two or more additional species.  It can be used to
 view multiple sequence alignment data, synteny or co-linearity data
 from other sources against genome annotations provided by GBrowse.
 GBrowse_syn is included with the standard GBrowse package (version 1.69 and
 later). Working examples can be seen at TAIR and WormBase.


Depends: tripal
Homepage: http://www.genome.clemson.edu/software/tripal
License: GPL ( as Drupal a derivative )
Pkg-Description: collection of Drupal modules for genomic research
 Tripal is a collection of open-source freely available Drupal modules under
 development at CUGI and a member of the GMOD family of tools. Tripal serve
 as a web interface for the GMOD Chado database. Tripal intially started as
 a web front-end for the Marine Genomics Project (MG.org). Work on the
 interface is currently ongoing for the MG.org project as well as the
 Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being
 implemented for the new Cacao Genome Database, and Citrus Genome Database
 and will be used for the Genome Database for Rosaceae. These latter three
 databases are projects of the Main Bioinformatics Laboratory at Washington
 State University

Depends: genemark
Homepage: http://exon.biology.gatech.edu/
License: Academic License Agreement
Pkg-Description: family of gene prediction programs
 A family of gene prediction programs developed at Georgia Institute of
 Technology, Atlanta, Georgia, USA.

Depends: python-orange
License: GPLv3
Homepage: http://orange.biolab.si/
Pkg-URL: http://orange.biolab.si/debian/
Responsible: Mitar <mmitar@gmail.com>
Pkg-Description: Data mining framework
 Orange is a component-based data mining software. It includes a range
 of data visualization, exploration, preprocessing and modeling
 techniques. It can be used through a nice and intuitive user interface
 or, for more advanced users, as a module for Python programming language.

Depends: tigr-glimmer-mg

Comment: Several related R packages are listed at CRAN:
         http://cran.r-project.org/web/views/Genetics.html
Comment: There is a Gentoo page featuring some projects we do not have mentioned here:
         http://gentoo-overlays.zugaina.org/dberkholz/sci-biology.html.en
Comment: Phylogenie centric Ubuntu derivative with some additional derivatives
	 http://www.eve.ucdavis.edu/rcthomson/phylis/
Comment: SEQanswers: The next generation sequencing community
	 http://seqanswers.com/forums/showthread.php?t=43
Comment: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)