Debian Med Project
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Summary
Biology development
Debian Med packages for development of bioinformatics applications

This metapackage will install Debian packages which might be helpful for development of applications for biological research.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Biology development packages

Official Debian packages with high relevance

Bioperl
Perl tools for computational molecular biology
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The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. It is well-accepted throughout the community and used in many high-profile projects, e.g., Ensembl.

The recommended packages are needed to run some of the included binaries, for a detailed explanation including the specific Perl modules please see README.Debian.

The suggested package enhances the manual pages.

Please cite: Jason E Stajich, David Block, Kris Boulez, Steven E Brenner, Stephen A Chervitz, Chris Dagdigian, Georg Fuellen, James G R Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehvaslaiho, Chad Matsalla, Chris J Mungall, Brian I Osborne, Matthew R Pocock, Peter Schattner, Martin Senger, Lincoln D Stein, Elia Stupka, Mark D Wilkinson and Ewan Birney: The Bioperl toolkit: Perl modules for the life sciences.. (PubMed,eprint) Genome Res. 12(10):1611-1618 (2002)
Bioperl-run
BioPerl wrappers: scripts
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Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

The package is enhanced by the following packages: clustalw exonerate kalign mcl phyml
Biosquid
utilities for biological sequence analysis
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SQUID is a library of C code functions for sequence analysis. It also includes a number of small utility programs to convert, show statistics, manipulate and do other functions on sequence files.

The original name of the package is "squid", but since there is already a squid on the archive (a proxy cache), it was renamed to "biosquid".

This package contains some tools to demonstrate the features of the SQUID library.

Libai-fann-perl
Perl wrapper for the FANN library
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This module provides a Perl wrapper for the Fast Artificial Neural Network (FANN) library (http://leenissen.dk/fann/wp/).

The AI::FANN object oriented interface provides an almost direct map to the C library API.

Libbio-mage-perl
Container module for classes in the MAGE package: MAGE
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MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the Microarray Gene Expression Data Society (MGED). This package contains Perl modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum Information About a Microarray Experiment) records of microarray ("DNA chips") experiments.

The Bio::MAGE module contains the following Bio::MAGE classes:

  • NameValueType
  • Extendable
  • Identifiable
  • Describable
Libbiojava-java
Java API to biological data and applications (default version)
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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is provided by a vibrant community which meets annually at the Bioinformatics Open Source Conference (BOSC) that traditionally accompanies the Intelligent Systems in Molecular Biology (ISMB) meeting. Much like BioPerl, the employment of this library is valuable for everybody active in the field because of the many tricks of the trade one learns just by communicating on the mailing list.

This is a wrapper package which should enable smooth upgrades to new versions.

Please cite: R. C. G. Holland, T. Down, M. Pocock, A. Prlićand D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer and M. J. Schreiber: BioJava: an Open-Source Framework for Bioinformatics. (PubMed,eprint) Bioinformatics 24(18):2096-2097 (2008)
Libbiojava3-java
Java API to biological data and applications (default version)
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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is provided by a vibrant community which meets annually at the Bioinformatics Open Source Conference (BOSC) that traditionally accompanies the Intelligent Systems in Molecular Biology (ISMB) meeting. Much like BioPerl, the employment of this library is valuable for everybody active in the field because of the many tricks of the trade one learns just by communicating on the mailing list.

This is a wrapper package which should enable smooth upgrades to new versions.

Libbiojava4-java
Java API to biological data and applications (default version)
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BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating sequences, file parsers, server support, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is provided by a vibrant community which meets annually at the Bioinformatics Open Source Conference (BOSC) that traditionally accompanies the Intelligent Systems in Molecular Biology (ISMB) meeting. Much like BioPerl, the employment of this library is valuable for everybody active in the field because of the many tricks of the trade one learns just by communicating on the mailing list.

This is a wrapper package which should enable smooth upgrades to new versions.

Libfreecontact-perl
fast protein contact predictor - binding for Perl
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the Perl binding.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Libfreecontact0-dev
fast protein contact predictor library - development files
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains files necessary for developing applications with libfreecontact.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Libgenome-1.3-dev
toolkit for developing bioinformatic related software (devel)
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libGenome is a freely available toolkit for developing bioinformatic related software in C++. It is intended to take the hassle out of performing common tasks on genetic sequence and annotation data. .. Among other things, libGenome can help you: ..

  • Read and write Multi-FastA format files
  • Read and write GenBank flat file database entries
  • Append, chop, truncate, reverse, complement, translate, and otherwise mangle sequence data
  • Access annotation in GenBank flat files

This is the development package containing the statically linked library and the header files.

Libgo-perl
perl modules for GO and other OBO ontologies
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This is a collection of perl code for dealing with Gene Ontologies (GO) and Open Biomedical Ontologies (OBO) style ontologies. It is part of the ‘go-dev’ distribution, but this Debian package is made from the CPAN archive. This package contains both scripts (which can be used with no knowledge of perl), and libraries which will be of use to perl programmers using GO or OBO.

Libhtsjdk-java
Java API for high-throughput sequencing data (HTS) formats
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HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM (Sequence Alignment/Map) and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

Libmems-1.6-dev
development library to support DNA string matching and comparative genomics
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libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements.

This is the development package containing the statically linked library and the header files.

Libmuscle-3.7-dev
multiple alignment development library for protein sequences
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MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there.

This library was derived from the original MUSCLE and turned into a library.

This package contains the static library and header files.

Libncbi6-dev
NCBI libraries for biology applications (development files)
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This package supplies development versions of NCBI's non-graphical C libraries, along with the corresponding header files.

Libnhgri-blastall-perl
Perl extension for running and parsing NCBI's BLAST 2.x
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NHGRI::Blastall will enable usage of BLAST out of a Perl script, if BLAST2 or WU-BLAST are installed locally. Main features are:

  • run BLAST (also via network, which requires blastcl3)
  • BLAST single sequences against each other or against a given library
  • format databases
  • mask out repetitive DNA
  • read, parse and filter existing BLAST reports
Libtfbs-perl
scanning DNA sequence with a position weight matrix
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The TFBS perl modules comprise a set of routines to interact with the Transfac and Jaspar databases that describe a special family of proteins, the transcription factors. These bind to genomic DNA to initiate (or prevent) the readout of a gene. Once multiple binding sites are known for a transcription factor, these are gathered in a single file and are aligned in order to find position-specific characteristica that might be used to predict such binding events in novel DNA sequences.

If you use TFBS in your work, please cite "Lenhard B., Wasserman W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics 18:1135-1136".

Please cite: Boris Lenhard and Wyeth W. Wasserman: TFBS: Computational framework for transcription factor binding site analysis. (PubMed) Bioinformatics 18(8):1135-1136 (2002)
Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
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Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic biological applications.

Mcl
Markov Cluster algorithm
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The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments.

MCL is currently being used in sciences like biology (protein family detection, genomics), computer science (node clustering in Peer-to-Peer networks), and linguistics (text analysis).

The package is enhanced by the following packages: zoem
Please cite: Stijn van Dongen and Cei Abreu-Goodger: Using MCL to extract clusters from networks. (PubMed,eprint) Methods Mol Biol. 804:281-95 (2012)
Python-biopython
Python library for bioinformatics (implemented in Python 2)
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The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. The project works along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project.

This package is targeting Python version 2.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python-cogent
framework for genomic biology
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PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for:

  • controlling third-party applications,
  • devising workflows; querying databases,
  • conducting novel probabilistic analyses of biological sequence evolution, and
  • generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.
Please cite: Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, J Gregory Caporaso, Brett C Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying and Gavin A Huttley: PyCogent: a toolkit for making sense from sequence. (PubMed,eprint) Genome Biology 8(8):R171 (2007)
Python-screed
short nucleotide read sequence utils in Python 2
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Screed parses FASTA and FASTQ files, generates databases, and lets you query these databases. Values such as sequence name, sequence description, sequence quality, and the sequence itself can be retrieved from these databases.

This is the Python 2 version.

Python3-cutadapt
Clean biological sequences from high-throughput sequencing reads
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Cutadapt helps with biological sequence clean tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Please cite: Marcel Martin: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1) (2015)
R-cran-genetics
GNU R package for population genetics
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Classes and methods for handling genetic data. Includes The package provides a library for the statistics environment R that contains classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, and more.

NOTE: THIS PACKAGE IS NOW OBSOLETE.

The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for information.

R-cran-haplo.stats
GNU R package for haplotype analysis
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The package provides routines for the GNU R statistics environment for statistical Analysis of indirectly measured Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap.

R-cran-rncl
GNU R interface to the Nexus Class Library
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This R package provides an interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.

R-cran-rnexml
GNU R package for semantically rich I/O for the 'NeXML' format
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Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.

Ruby-bio
Ruby tools for computational molecular biology
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BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.

Official Debian packages with lower relevance

Libfreecontact-doc
documentation for libfreecontact
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FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains HTML documentation for libfreecontact.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Python-biopython-doc
Documentation for the Biopython library
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Documentation and examples about how to use the Biopython library.

This package also contains the unit tests of the test suite to enable reproducing the test results.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python-biopython-sql
Biopython support for the BioSQL database schema (Python 2)
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This is the Biopython interface to a BioSQL database (see www.biosql.org for details). BioPerl, BioJava and BioRuby also provide their own BioSQL interfaces onto the same shared SQL schema.

This package is targeting Python version 2.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python-cutadapt
Clean biological sequences from high-throughput sequencing reads
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Cutadapt helps with biological sequence clean tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Please cite: Marcel Martin: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1) (2015)
Python3-biopython
Python library for bioinformatics (implemented in Python 3)
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The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. The project works along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project.

This package is targeting Python version 3.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
Python3-biopython-sql
Biopython support for the BioSQL database schema (Python 3)
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This is the Biopython interface to a BioSQL database (see www.biosql.org for details). BioPerl, BioJava and BioRuby also provide their own BioSQL interfaces onto the same shared SQL schema.

This package is targeting Python version 3.

Please cite: Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski and Michiel J. L. de Hoon: Biopython: freely available Python tools for computational molecular biology and bioinformatics. (PubMed,eprint) Bioinformatics 25(11):1422-1423 (2009)
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