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.

Libace-perl
Object-Oriented Access to ACEDB Databases
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AcePerl is an object-oriented Perl interface for the AceDB database. It provides functionality for connecting to remote AceDB databases, performing queries, fetching ACE objects, and updating databases. The programmer's API is compatible with the JADE Java API, and interoperable with the API used by BoulderIO.

AceDB is a genome database system developed since 1989 primarily by Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger Institute). It was originally developed for the C.elegans genome project , from which its name was derived (A C. elegans DataBase).

Please cite: Lincoln D. Stein and Jean Thierry-Mieg: Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases. (PubMed,eprint) Genome Research 8(12):1308-1315 (1998)
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.

Libbambamc-dev
Development files for reading and writing BAM (genome alignment) files
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The BAM Format is a binary format for storing sequence data. This is a lightweight C implementation of the read name collation code from the larger bambam C++ project to handle BAM file input and BAM file output.

This package contains the static library and header files.

Libbamtools-dev
C++ API for manipulating BAM (genome alignment) files
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BamTools facilitates research analysis and data management using BAM files. It copes with the enormous amount of data produced by current sequencing technologies that is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

BamTools provides both a C++ API for BAM file support as well as a command-line toolkit.

This is the developers API package.

Please cite: Derek W. Barnett, Erik K. Garrison, Aaron R. Quinlan, Michael P. Stromberg and Gabor T. Marth: BamTools: a C++ API and toolkit for analyzing and managing BAM files. (PubMed,eprint) Bioinformatics 27(12):1691-2 (2011)
Libbio-das-lite-perl
implementation of the BioDas protocol
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Bio::Das::Lite is an implementation of the BioDas protocol for the retrieval of biological data from XML sources over HTTP.

Bio::Das::Lite is designed as a lightweight and more forgiving alternative to the client/retrieval/parsing components of Bio::Das. Bio::Das::Lite itself is not a drop-in replacement for Bio::Das but it can be subclassed to do so.

Libbio-graphics-perl
Generate GD images of Bio::Seq objects
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The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature, Das::Segment::Feature and Bio::DB::Graphics objects. It can be used to draw sequence annotations, physical (contig) maps, protein domains, or any other type of map in which a set of discrete ranges need to be laid out on the number line.

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
Libbio-mage-utils-perl
Extra modules 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.

Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology, as well as SQL utilities.

Libbio-primerdesigner-perl
Perl module to design PCR primers using primer3 and epcr
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Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. In addition to accessing local installations of primer3 or e-PCR, it also offers the ability to accessing the primer3 binary via a remote server.

Libbiococoa-dev
Bioinformatics framework for GNUstep and Cocoa (development files)
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BioCocoa is an open source Cocoa framework for bioinformatics. It intends to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications.

This package contains the development files, documentation and examples for developing GNUstep applications using the BioCocoa framework.

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.

Libblasr-dev
tools for aligning PacBio reads to target sequences (development files)
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Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment.

This package contains the header files and static library for the alignment sublibrary.

Libbpp-core-dev
Bio++ Core library development files
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

This package contains the static library and the header files of the Bio++ core classes.

Libbpp-phyl-dev
Bio++ Phylogenetic library development files
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

This package contains the static library and the header files ofthe Bio++ classes for phylogenetics.

Libbpp-phyl-omics-dev
Bio++ Phylogenetics library: genomics components (development files)
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

This package contains the static library and the header files of the Bio++ classes dedicated to genomic phylogeny.

Libbpp-popgen-dev
Bio++ Population Genetics library development files
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

This package contains the static library and the header files of the Bio++ Population Genetics classes.

Libbpp-qt-dev
Bio++ Qt Graphic classes library development files
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

Contains development files of the Bio++ graphical classes developed with Qt.

Libbpp-raa-dev
Bio++ Remote Acnuc Access library development files
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This library contains utilitary and classes to query public databases (GenBank, EMBL, SwissProt, etc) using acnuc. It is part of the Bio++ project.

This package contains header files and static library.

Libbpp-seq-dev
Bio++ Sequence library development files
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

This package contains the static library and the header files of Bio++ classes for sequence analysis classes.

Libbpp-seq-omics-dev
Bio++ Sequence library: genomics components
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Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

This package contains the static library and the header files of the Bio++ classes dedicated to genomic sequencing.

Libchado-perl
database schema and tools for genomic data
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Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

Libconsensuscore-dev
algorithms for PacBio multiple sequence consensus -- development files
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ConsensusCore is a library of C++ algorithms for Pacific Biosciences multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET). This library primarily exists as the backend for GenomicConsensus, which implements Quiver.

This package is part of the SMRT Analysis suite. It provides the header files and static library.

Libdivsufsort-dev
libdivsufsort header files
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The libdivsufsort project provides a fast, lightweight, and robust C API library to construct the suffix array and the Burrows-Wheeler transformed string for any input string of a constant-size alphabet.

This package installs files needed for development.

Libfast5-dev
library for reading Oxford Nanopore Fast5 files -- headers
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A lightweight C++11 library to read raw signal data from Oxford Nanopore's FAST5 files.

This package provides the header files for development with fast5.

Libfastahack-dev
library for indexing and sequence extraction from FASTA files (devel)
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fastahack is a small application for indexing and extracting sequences and subsequences from FASTA files. The included Fasta.cpp library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.

Features:

  • FASTA index (.fai) generation for FASTA files
  • Sequence extraction
  • Subsequence extraction
  • Sequence statistics (currently only entropy is provided)

Sequence and subsequence extraction use fseek64 to provide fastest-possible extraction without RAM-intensive file loading operations. This makes fastahack a useful tool for bioinformaticists who need to quickly extract many subsequences from a reference FASTA sequence.

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

Libffindex0-dev
library for simple index/database for huge amounts of small files (development)
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FFindex is a very simple index/database for huge amounts of small files. The files are stored concatenated in one big data file, separated by '\0'. A second file contains a plain text index, giving name, offset and length of the small files. The lookup is currently done with a binary search on an array made from the index file.

This package contains the header files and documentation needed to develop applications with libffindex.

Libfml-dev
development headers for libfml
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Fermi-lite is a standalone C library tool for assembling Illumina short reads in regions from 100bp to 10 million bp in size.

This package contains the C library headers for using libfml in custom tools, along with a static library.

Libfreecontact-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?)
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?)
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.

Libgenome-model-tools-music-perl
module for finding mutations of significance in cancer
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The MuSiC suite is a set of tools aimed at discovering the significance of somatic mutations found within a given cohort of cancer samples, and with respect to a variety of external data sources.

Libgenome-perl
pipelines, tools, and data management for genomics
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This is the base namespace module for the Genome software tree.

That tree has several primary components:

Genome::Model: a data modeling pipeline management system for genomics

Genome::Model::Tools a tree of >1000 tools and tool wrappers for genomics

Genome::* a variety of sample tracking classes with an RDBMS back-end

Only the tools system is currently released.

See genome for a complete inventory of all tool packages, and for command-line access to those tools.

Libgenometools0-dev
development files for GenomeTools
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This package contains the GenomeTools static library and necessary header files.

Besides basic bioinformatics data structures, the library contains components for sequence and annotation handling, sequence compression, index structure generation and access, efficient matching, annotation visualization and much more.

Please cite: Gordon Gremme, Sascha Steinbiss and Stefan Kurtz: GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.. (PubMed) IEEE/ACM Transactions on Computational Biology and Bioinformatics 10(3):645-656 (2013)
Libgff-dev
GFF/GTF parsing from cufflinks as a library
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This is a simple "libraryfication" of the GFF/GTF parsing code that is used in the Cufflinks codebase. There are not many (any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, and the goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.

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.

Libhmsbeagle-dev
High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
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BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.

The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution.

The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units.

This package contains development files needed to build against Beagle library.

Please cite: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics. (PubMed,eprint) Systematic Biology 61(1):170-3 (2012)
Libhts-dev
Development files for the HTSlib
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HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent.

This package contains development files for the HTSlib: headers, static library, manual pages, etc.

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.

Libjebl2-java
Java Evolutionary Biology Library
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A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees.

This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library.

Remark of Debian Med team: Fork from jebl

This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library.

Libkmer-dev
suite of tools for DNA sequence analysis (development lib)
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The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); aligning (ESTs, mRNAs, whole genomes); and a variety of analyses based on kmers.

This is a metapackage package depending on the development components of kmer.

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.

Libminimap-dev
development headers for libminimap
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Minimap is an experimental tool to efficiently find multiple approximate mapping positions between two sets of long sequences, such as between DNA reads and reference genomes, between genomes and between long noisy reads.

This package contains the C library headers for using minimap in custom tools, along with a static library.

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.

Libncbi-vdb-dev
libraries for using data in the INSDC Sequence Read Archives (devel)
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Much of the data submitted these days, for example in BAM, Illumina export.txt, and Complete Genomics formats, contain alignment information. With aligned data, NCBI uses Compression by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, for example as FastQ, requires fast access to the reference sequences that the original data was aligned to. NCBI recommends that SRA users dedicate local disk space to store references downloaded from the NCBI SRA site. As of Fall 2014, the complete collection of these reference sequences is 66 GB. While it isn't usually necessary to download the entirety of the reference sequences, this should give you an idea of the scale of the storage requirement. By default, the Toolkit will download missing reference sequences on demand and cache them in the user's home directory. The location of this cache is configurable, as is whether the download is automatic or manual.

This is the development package.

Libncbi6-dev
NCBI libraries for biology applications (development files)
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Debtags of package libncbi6-dev:
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This package supplies development versions of NCBI's non-graphical C libraries, along with the corresponding header files.

Libncl-dev
NEXUS Class Library (static lib and header files)
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The NEXUS Class Library is a C++ library for parsing NEXUS files.

The NEXUS file format is widely used in bioinformatics. Several popular phylogenetic programs such as Paup, MrBayes, Mesquite, and MacClade use this format.

This package contains the static library and header files of the NEXUS library.

Libngs-java
Next Generation Sequencing language Bindings (Java bindings)
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NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb.

The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.

Java bindings.

Libngs-sdk-dev
Next Generation Sequencing language Bindings (development)
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NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb.

The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.

This is the development package.

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
Libopenms-dev
library for LC/MS data management and analysis - dev files
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OpenMS is a library for LC/MS data management and analysis. OpenMS offers an infrastructure for the development of mass spectrometry-related software and powerful 2D and 3D visualization solutions.

OpenMS offers analyses for various quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM, SWATH…

It provides built-in algorithms for de-novo identification and database search, as well as adapters to other state-of-the art tools like X!Tandem, Mascot, OMSSA…

OpenMS supports the Proteomics Standard Initiative (PSI) formats for MS data and supports easy integration of tools into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept and a unified parameter handling.

This package ships the library development files.

Please cite: Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert and Oliver Kohlbacher: OpenMS – an Open-Source Software Framework for Mass Spectrometry. (PubMed,eprint) BMC Bioinformatics 9(163) (2008)
Libpal-java
Phylogenetic Analysis Library
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The PAL project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. At present PAL consists of approximately 200 public classes/interfaces in 16 packages Please refer to the API documentation for a detailed description of all classes and methods available, and to the release history for an overview of the development history of PAL.

Please cite: Alexei Drummond and Korbinian Strimmer: PAL: an object-oriented programming library for molecular evolution and phylogenetics. (PubMed,eprint) Bioinformatics 17(7):662-663 (2001)
Libpbbam-dev
Pacific Biosciences binary alignment/map (BAM) library (headers)
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The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. The specifications for BAM/SAM are maintained by the SAM/BAM Format Specification Working Group.

PacBio-produced BAM files are fully compatible with the BAM specification, but makes use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information. The pbbam library provides tools to work with these files

This package contains the library header files.

Libpbdata-dev
tools for handling PacBio sequences (development files)
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Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment.

This package contains the header files and static library for the pbdata sublibrary.

Libpbihdf-dev
tools for handling PacBio hdf5 files (development files)
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Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment.

This package contains the header files and static library for the hdf sublibrary.

Libpbseq-dev
library for analyzing PacBio sequencing data (development files)
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Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment.

This is a metapackage that depends on the pbseqlib component development files.

Libqes-dev
DNA sequence parsing library -- development
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A small C library, with a bioinformatic focus. Optimised for speed and a clean API. Handles sequence parsing and miscellaneous manipulation of DNA sequences.

These are the development headers required to use libqes in your own applications.

Librcsb-core-wrapper0-dev
development files for librcsb-core-wrapper0
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The RCSB Core Wrapper library was developed to provide an object-oriented application interface to information in mmCIF format. It includes several classes for accessing data dictionaries and mmCIF format data files.

This package contains files necessary for developing applications with the library.

The package is enhanced by the following packages: librcsb-core-wrapper0-dbg
Librdp-taxonomy-tree-java
taxonomy tree library from Ribosomal Database Project (RDP)
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The TaxonomyTree project is a library used by other Ribosomal Database Project (RDP) tools.

Librelion-dev
C++ API for RELION (3D reconstructions in cryo-electron microscopy)
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RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

RELION provides a GUI, several command-line tools in parallel (MPI) and serial versions as well as a C++ API.

This is the developers API package for use without GUI and MPI.

Please cite: Sjors H. W. Scheres: RELION: implementation of a Bayesian approach to cryo-EM structure determination. (PubMed) J Struct Biol. (3):519-30 (180)
Librg-blast-parser-perl
very fast NCBI BLAST parser - binding for Perl
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This package contains Perl binding for a very fast C++ library that parses the default output of NCBI BLAST programs. BLAST results are returned in a convenient hash structure.

Evaluated on a very small test set, this parser is considerably faster than Zerg::Report from libzerg-perl.

Librg-reprof-bundle-perl
protein secondary structure and accessibility predictor (perl module)
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'reprof' is an improved implementation of 'prof', a popular protein secondary structure and accessibility predictor. Prediction is either done from protein sequence alone or from an alignment - the latter should be used for optimal performance.

This package provides the perl modules implementing 'reprof' along with the necessary data files.

Librostlab-blast0-dev
very fast C++ library for parsing the output of NCBI BLAST programs (devel)
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This package provides a very fast library for parsing the default output of NCBI BLAST programs into a C++ structure.

libzerg is faster, but it provides only lexing (i.e. it only returns pairs of token identifiers and token string values). librostlab-blast uses a parser generated with bison on top of a flex-generated lexer very similar to that of libzerg.

This package contains files necessary for developing applications with librostlab-blast.

Librostlab3-dev
C++ library for computational biology (development)
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This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products.

The library provides the following facilities:

  • current working directory resource
  • exception with stack backtrace
  • file lock resource
  • passwd and group structures for C++
  • effective uid and gid resource
  • rostlab::bio::seq class with stream input operator for FASTA format
  • umask resource

This package contains files necessary for developing applications with librostlab.

Libsbml5-dev
System Biology Markup Language library - development files
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LibSBML is a library designed to help you read, write, manipulate, translate, and validate SBML files and data streams. It is not an application itself (though it does come with many example programs), but rather a library you can embed in your own applications.

This package contains files necessary for development with libsbml.

Please cite: Benjamin J Bornstein, Sarah M Keating, Akiya Jouraku and Michael Hucka: LibSBML: An API Library for SBML. (PubMed,eprint) Bioinformatics 24(6):880-881 (2008)
Libsmithwaterman-dev
determine similar regions between two strings or genomic sequences (devel)
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The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings or nucleotide or protein sequences. Instead of looking at the total sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.

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

Libsnp-sites1-dev
Static libraries and header files for the package snp-sites
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Snp-sites finds single nucleotide polymorphism (SNP) sites from multi-fasta alignment input files (which might be compressed). Its output can be in various widely used formats (Multi Fasta Alignment, Vcf, phylip).

The software has been developed at the Wellcome Trust Sanger Institute.

This package contains the development files to include snp-sites into your own code. The library enables Python developers to make snp-sites function calls (Python bindings) through the Boost Python Library.

Please cite: Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane and Simon R. Harris: SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. (eprint) Microbial Genomics 2(4) (2016)
Libsort-key-top-perl
Perl module to select and sort top n elements of a list
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The functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.

They are all variations around 'keytopsort { CALC_KEY($_) } $n => @data;'.

In array context, this function calculates the ordering key for every element in @data using the expression inside the block. Then it selects and orders the $n elements with the lower keys when compared lexicographically.

In scalar context, the value returned by the functions on this module is the cutoff value allowing to select nth element from the array.

Libsrf-dev
C++ implementation of the SRF format for DNA sequence data
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SRF (sort for Sequence Read Format) is a generic format capable of storing data generated by any DNA sequencing technology. This library is an implementation of SRF and provides basic input-output functions.

Libssm-dev
macromolecular superposition library - development files
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SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI.

The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms.

The algorithm implemented by the software is described in: E. Krissinel & K. Henrick (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. 60, 2256-68.

This package contains libraries and header files needed for program development.

Please cite: E. Krissinel and K. Henrick: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. (PubMed,eprint) Acta Crystallogr D Biol Crystallogr. 60(1):2256-68 (2004)
Libssw-dev
Development headers and static libraries for libssw
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This package provides development headers and static libraries for libssw, a fast implementation of the Smith-Waterman algorithm using Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level.

Please cite: Mengyao Zhao, Wan-Ping Lee, Erik P. Garrison and Gabor T. Marth: SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications.. (eprint) PLoS One 8:e82138 (2013)
Libssw-java
Java bindings for libssw
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This package provides JNI based Java bindings for libssw, a fast implementation of the Smith-Waterman algorithm using Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level.

Please cite: Mengyao Zhao, Wan-Ping Lee, Erik P. Garrison and Gabor T. Marth: SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications.. (eprint) PLoS One 8:e82138 (2013)
Libstaden-read-dev
development files for libstaden-read
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This package contains the header and development files needed to build programs and packages using the Staden io_lib.

The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.

Libtabixpp-dev
C++ wrapper to tabix indexer (development files)
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This package provides development headers and static libraries for libtabixpp, a C++ interface wrapper for Tabix. Tabix is a part of htslib to index tabular files in which some columns indicate sequence coordinates.

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.

Libzerg-perl
fast perl module for parsing the output of NCBI BLAST programs
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The Zerg library contains a C/flex lexical scanner for BLAST reports and a set of supporting functions. It is centered on a "get_token" function that scans the input for specified lexical elements and, when one is found, returns its code and value to the user.

It is intended to be fast: for that the authors used flex, which provides simple regular expression matching and input buffering in the generated C scanner. And it is intended to be simple in the sense of providing just a lexical scanner, with no features whose support could slow down its main function.

Please cite: Apuã C M Paquola, Abimael A Machado, Eduardo M Reis, Aline M Da Silva and Sergio Verjovski-Almeida: Zerg: a very fast BLAST parser library. (PubMed,eprint) Bioinformatics 19(8):1035-6 (2003)
Libzerg0-dev
development libraries and header files for libzerg
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Zerg is a C library for lexing - lexically scanning - the output of NCBI BLAST programs.

Based on a GNU Flex-generated lexical scanner, it runs extremely fast, being especially useful for processing large volumes of data. Benchmark tests show that Zerg is over two orders of magnitude faster than some widely used BLAST parsers.

If you need a parser and not only a lexer, check out librostlab-blast.

This package contains the header files and documentation needed to develop applications with libzerg.

Please cite: Apuã C M Paquola, Abimael A Machado, Eduardo M Reis, Aline M Da Silva and Sergio Verjovski-Almeida: Zerg: a very fast BLAST parser library. (PubMed,eprint) Bioinformatics 19(8):1035-6 (2003)
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)
Octave-bioinfo
bioinformatic functions for Octave
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This package provides functions to do work in bioinformatics in Octave, a numerical computation software. It contains functions to convert amino acid characters into integers (aa2int), convert between amino acid representations (aminolookup), cleave peptides (cleave), convert integers into amino acid characters (int2aa) and reverse a nucleotide sequence (seqreverse).

This Octave add-on package is part of the Octave-Forge project.

Remark of Debian Med team: Not maintained upstream, see ROM: #620648
Pyfai
Fast Azimuthal Integration scripts
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PyFAI is a Python library for azimuthal integration; it allows the conversion of diffraction images taken with 2D detectors like CCD cameras into X-Ray powder patterns that can be used by other software like Rietveld refinement tools (i.e. FullProf), phase analysis or texture analysis.

As PyFAI is a library, its main goal is to be integrated in other tools like PyMca, LiMa or EDNA. To perform online data analysis, the precise description of the experimental setup has to be known. This is the reason why PyFAI includes geometry optimization code working on "powder rings" of reference samples. Alternatively, PyFAI can also import geometries fitted with other tools like Fit2D.

PyFAI has been designed to work with any kind of detector with any geometry (transmission, reflection, off-axis, ...). It uses the Python library FabIO to read most images taken by diffractometer.

Python-biom-format
Biological Observation Matrix (BIOM) format (Python 2)
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The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.

The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.

This package provides the BIOM format library for the Python 2 interpreter.

Please cite: Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai R. Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight and J. G. Caporaso: The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. (eprint) GigaScience 1:7 (2012)
Python-cobra
constraint-based modeling of biological networks (Python 2)
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COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accommodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux balance analysis, flux variability analysis, and gene deletion analyses.

This package provides the Python 2 module.

Please cite: Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson and Daniel R Hyduke: COBRApy: COnstraints-Based Reconstruction and Analysis for Python. (PubMed) BMC Systems Biology 7(74) (2013)
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-corepywrap
library that exports C++ mmCIF accessors to Python
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The RCSB Core Wrapper library was developed to provide an object-oriented application interface to information in mmCIF format. It includes several classes for accessing data dictionaries and mmCIF format data files.

This library provides Python bindings for librcsb-core-wrapper.

The package is enhanced by the following packages: librcsb-core-wrapper0-dbg
Python-freecontact
fast protein contact predictor - binding for Python
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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 Python binding.

Please cite: László Kaján, Thomas A. Hopf, Matúš Kalaš, Debora S. Marks and Burkhard Rost: FreeContact: ... BMC Bioinformatics (201?)
Python-htseq
high-throughput genome sequencing read analysis utilities
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HTSeq can be used to performing a number of common analysis tasks when working with high-throughput genome sequencing reads:

  • Getting statistical summaries about the base-call quality scores to study the data quality.
  • Calculating a coverage vector and exporting it for visualization in a genome browser.
  • Reading in annotation data from a GFF file.
  • Assigning aligned reads from an RNA-Seq experiments to exons and genes.
Please cite: Simon Anders, Paul Theodor Pyl and Wolfgang Huber: HTSeq—a Python framework to work with high-throughput sequencing data. (PubMed,eprint) Bioinformatics 31(2):166-169 (2015)
Python-kineticstools
detection of DNA modifications (Python 2 library)
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Tools for detecting DNA modifications from single molecule, real-time (SMRT®) sequencing data. This tool implements the P_ModificationDetection module in SMRT® Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol. Researchers interested in understanding or extending the modification detection algorithms can use these tools as a starting point.

This package is part of the SMRTAnalysis suite and contains the backend Python 2 library.

Python-mmtk
molecular modeling toolkit
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The Molecular Modeling Toolkit (MMTK) is a library for molecular simulation applications. It provides the most common methods in molecular simulations (molecular dynamics, energy minimization, normal mode analysis) and several force fields used for biomolecules (Amber 94, Amber 99, several elastic network models). MMTK also serves as a code basis that can be easily extended and modified to deal with non-standard situations in molecular simulations.

Python-pbcommand
common command-line interface for Pacific Biosciences analysis modules
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To integrate with the pbsmrtpipe workflow engine, one must to be able to generate a Tool Contract and to be able to run from a Resolved Tool Contract. A Tool Contract contains the metadata of the exe, such as the file types of inputs, outputs and options. There are two principal use cases, first wrapping/calling Python functions that have been defined in external Python packages, or scripts. Second, creating a CLI tool that supports emitting tool contracts, running resolved tool contracts and complete argparse-style CLI.

Python-pbcore
Python library for processing PacBio data files
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The pbcore package provides Python modules for processing Pacific Biosciences data files and building PacBio bioinformatics applications. These modules include tools to read/write PacBio data formats, sample data files for testing and debugging, base classes, and utilities for building bioinformatics applications.

This package is part of the SMRTAnalysis suite.

Python-pbh5tools
tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
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This package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers. cmp.h5 files contain alignment information while bas.h5 files contain base-call information.

pbh5tools is part of the SMRTAnalysis suite. This package provides the Python 2 backend library

Python-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 2)
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Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

This package installs the module for Python 2.

The package is enhanced by the following packages: python-pysam-tests
Python-rdkit
Collection of cheminformatics and machine-learning software
Maintainer: Debichem Team
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RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include:

  • Chemical reaction handling and transforms
  • Substructure searching with SMARTS
  • Canonical SMILES
  • Molecule-molecule alignment
  • Large number of molecular descriptors, including topological, compositional, EState, SlogP/SMR, VSA and Feature-map vectors
  • Fragmentation using RECAP rules
  • 2D coordinate generation and depiction, including constrained depiction
  • 3D coordinate generation using geometry embedding
  • UFF and MMFF94 forcefields
  • Chirality support, including calculation of (R/S) stereochemistry codes
  • 2D pharmacophore searching
  • Fingerprinting, including Daylight-like, atom pairs, topological torsions, Morgan alogrithm and MACCS keys
  • Calculation of shape similarity
  • Multi-molecule maximum common substructure
  • Machine-learning via clustering and information theory algorithms
  • Gasteiger-Marsili partial charge calculation

File formats RDKit supports include MDL Mol, PDB, SDF, TDT, SMILES and RDKit binary format.

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-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-consensuscore2
generate consensus sequences for PacBio data -- Python 3
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ConsensusCore2 embodies core C++ routines underlying the Arrow HMM algorithm for PacBio multi-sequence consensus. Arrow is the successor to the Quiver model---a CRF model that was embodied in the ConsensusCore C++ library. Compared to Quiver, the Arrow model is more statistically principled and easier and more robust to train.

This package installs the library for Python 3.

Python3-csb
Python framework for structural bioinformatics (Python3 version)
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Computational Structural Biology Toolbox (CSB) is a Python class library for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.

CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice.

This is the Python3 version of the package.

Python3-cutadapt
Clean biological sequences from high-throughput sequencing reads (Python 3)
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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.

This package contains the Python 3 module.

Please cite: Marcel Martin: Cutadapt removes adapter sequences from high-throughput sequencing reads. (eprint) EMBnet.journal 17(1):10-12 (2015)
Python3-dendropy
DendroPy Phylogenetic Computing Library (Python 3)
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DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the library. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting “glue” that assembles and drives such pipelines.

This package provides python3 modules.

Please cite: Jeet Sukumaran and Mark T. Holder: DendroPy: a Python library for phylogenetic computing. (PubMed,eprint) Bioinformatics 26(12):1569-1571 (2010)
Python3-hyphy
Hypothesis testing using Phylogenies (Python 3 module)
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HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.

This package provides files the Python 3 module.

Please cite: Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse: HyPhy: hypothesis testing using phylogenies. (PubMed,eprint) Bioinformatics 21(5):676-679 (2005)
Python3-ngs
Next Generation Sequencing language Bindings (Python3 bindings)
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NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb.

The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.

Python3 bindings.

Python3-pbconsensuscore
algorithms for PacBio multiple sequence consensus -- Python 3
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ConsensusCore is a library of C++ algorithms for Pacific Biosciences multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET). This library primarily exists as the backend for GenomicConsensus, which implements Quiver.

This package is part of the SMRT Analysis suite. It provides the Python3 bindings.

Python3-pyfaidx
efficient random access to fasta subsequences for Python 3
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Samtools provides a function "faidx" (FAsta InDeX), which creates a small flat index file ".fai" allowing for fast random access to any subsequence in the indexed FASTA file, while loading a minimal amount of the file in to memory. This Python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script "faidx" is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge.

This package provides the Python 3 modules to access fasta files.

Please cite: Matthew D. Shirley, Zhaorong Ma, Brent S. Pedersen and Sarah J. Wheelan: Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196 (2015)
Python3-pymummer
Python 3 interface to MUMmer
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pymummer is a Python wrapper for running the programs of the MUMmer sequence alignment suite and parsing their output.

Python3-pyvcf
Variant Call Format (VCF) parser for Python 3
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The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project.

The intent of this module is to mimic the csv module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. vcf will attempt to parse the content of each record based on the data types specified in the meta-information lines -- specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings.

This package provides the Python 3 modules.

Python3-ruffus
Python3 computation pipeline library widely used in bioinformatics
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Ruffus is designed to allow scientific and other analyses to be automated with the minimum of fuss and the least effort.

  • Lightweight: Suitable for the simplest of tasks
  • Scalable: Handles even fiendishly complicated pipelines which would cause make or scons to go cross-eyed and recursive.
  • Standard Python: No "clever magic", no pre-processing.
  • Unintrusive: Unambitious, lightweight syntax which tries to do this one small thing well.

This package provides python3 modules.

Please cite: Leo Goodstadt: Ruffus: A Lightweight Python Library for Computational Pipelines. (PubMed,eprint) Bioinformatics 26(21):2778-9 (2010)
Python3-skbio
Python3 data structures, algorithms, educational resources for bioinformatic
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Scikit-bio is a Python package providing data structures, algorithms, and educational resources for bioinformatics.

This is the package for Python3

R-bioc-biobase
base functions for Bioconductor
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Biobase is part of the Bioconductor project, and is used by many other packages. Biobase contains standardized data structures to represent genomic data, and functions that are needed by many other packages or which replace R functions.

Bioconductor is a project to develop innovative software tools for use in computational biology. It is based on the R language. You should already be quite familiar with R before using Bioconductor. Bioconductor packages provide flexible interactive tools for carrying out a number of different computational tasks.

Please cite: Robert C Gentleman, Vincent J Carey, Douglas M Bates, Ben Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Iacus, Rafael Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony J Rossini, Gunther Sawitzki, Colin Smith, Gordon Smyth, Luke Tierney, Jean Y H Yang and Jianhua Zhang: Bioconductor: Open software development for computational biology and bioinformatics. (PubMed,eprint) Genome Biology 5(10):R80 (2004)
Remark of Debian Med team: This is a part of Bioconductor project

A nice overview about all modules of BioDonductor is given at http://www.bioconductor.org/packages/release/bioc/

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-phylobase
GNU R base package for phylogenetic structures and comparative data
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This R package provides a base S4 class for comparative methods, incorporating one or more trees and trait data as these are used in other packages dealing with phylogenetic structures and comparative data.

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.

Ruby-crb-blast
Run conditional reciprocal best blast
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CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.

CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by performing BLAST alignments of query->target and target->query. Reciprocal best BLAST hits are those where the best match for any given query sequence in the query->target alignment is also the best hit of the match in the reverse (target->query) alignment.

Reciprocal best BLAST is a very conservative way to assign orthologs. The main innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to each pairwise alignment by taking into account the overall relatedness of the two datasets being compared. This is done by fitting a function to the distribution of alignment e-values over sequence lengths. The function provides the e-value cutoff for a sequence of given length.

Sbmltoolbox
libsbml toolbox for octave and matlab
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The SBMLToolbox provides a set of basic functions for reading, writing, manipulating, and simulating SBML (System Biology Meta Language) models. It is a free Open Source package on top of the libSBML with full compatibility to work with MATLAB and Octave alike and share models between the two systems.

The toolbox is not a complete turn key solution for Systems Biology. It has its emphasis on easing the handling of SBML data and serves as a starting point for users and developers to establish their own methods.

Please cite: S. M. Keating, B. J. Bornstein, A. Finney and M. Hucka: SBMLToolbox: an SBML toolbox for MATLAB users.. (eprint) Bioinformatics 22(10):1275-1277 (2006)
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Seqan-dev
C++ library for the analysis of biological sequences (development)
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SeqAn is a C++ template library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.

This package contains the developer files, documentation and examples.

Please cite: Andreas Doring, David Weese, Tobias Rausch and Knut Reinert: SeqAn An efficient, generic C++ library for sequence analysis. (PubMed,eprint) BMC Bioinformatics 9(1):11 (2008)

Official Debian packages with lower relevance

Libbam-dev
manipulates nucleotide sequence alignments in BAM or SAM format
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The BAM library provides I/O and various operations on manipulating nucleotide sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region.

This library is part of SAMtools version 0.1.19. It is obsolete and provided only to build software that has not yet transitioned to the HTSlib, which replaces this library.

Libdisorder-dev
library for entropy measurement of byte streams (devel)
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This library provides a function to calculate the Shannon index (H) of byte streams.

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

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?)
Libgtextutils-dev
Gordon Text_utils library (development files)
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The Gordon Text_utils (gtextutils) library is a text utilities library used by the FASTX-Toolkit, a suite of programs for biological sequence analysis.

Development files for the Gordon Text_utils (gtextutils) library.

Librostlab-blast-doc
very fast C++ library for parsing the output of NCBI BLAST programs (doc)
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This package provides a very fast library for parsing the default output of NCBI BLAST programs into a C++ structure.

libzerg is faster, but it provides only lexing (i.e. it only returns pairs of token identifiers and token string values). librostlab-blast uses a parser generated with bison on top of a flex-generated lexer very similar to that of libzerg.

This package contains html and pdf documentation.

Librostlab-doc
C++ library for computational biology (documentation)
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This library was developed by the Rost Lab. The lab's research is driven by a conviction that protein and DNA sequences encode a significant core of information about the ultimate structure and function of genetic material and its gene products.

The library provides the following facilities:

  • current working directory resource
  • exception with stack backtrace
  • file lock resource
  • passwd and group structures for C++
  • effective uid and gid resource
  • rostlab::bio::seq class with stream input operator for FASTA format
  • umask resource

This package contains html documentation.

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-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-consensuscore2
generate consensus sequences for PacBio data -- Python 2
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ConsensusCore2 embodies core C++ routines underlying the Arrow HMM algorithm for PacBio multi-sequence consensus. Arrow is the successor to the Quiver model---a CRF model that was embodied in the ConsensusCore C++ library. Compared to Quiver, the Arrow model is more statistically principled and easier and more robust to train.

This package installs the library for Python 2.

Python-csb
Python framework for structural bioinformatics
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Computational Structural Biology Toolbox (CSB) is a Python class library for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.

CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice.

Python-cutadapt
Clean biological sequences from high-throughput sequencing reads (Python 2)
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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.

This package contains the Python 2 module.

Please cite: Marcel Martin: Cutadapt removes adapter sequences from high-throughput sequencing reads. (eprint) EMBnet.journal 17(1):10-12 (2015)
Python-dendropy
DendroPy Phylogenetic Computing Library (Python 2)
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DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the library. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting “glue” that assembles and drives such pipelines.

This package provides python2 modules.

Please cite: Jeet Sukumaran and Mark T. Holder: DendroPy: a Python library for phylogenetic computing. (PubMed,eprint) Bioinformatics 26(12):1569-1571 (2010)
Python-hyphy
Hypothesis testing using Phylogenies (Python 2 module)
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HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface) and it can be compiled as a shared library and called from other programming environments such as Python or R. Continued development of HyPhy is currently supported in part by an NIGMS R01 award 1R01GM093939.

This package provides files the Python 2 module.

Please cite: Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse: HyPhy: hypothesis testing using phylogenies. (PubMed,eprint) Bioinformatics 21(5):676-679 (2005)
Python-ngs
Next Generation Sequencing language Bindings (Python bindings)
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NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository ncbi-vdb.

The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.

Python bindings.

Python-pbconsensuscore
algorithms for PacBio multiple sequence consensus -- Python 2
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ConsensusCore is a library of C++ algorithms for Pacific Biosciences multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET). This library primarily exists as the backend for GenomicConsensus, which implements Quiver.

This package is part of the SMRT Analysis suite. It provides the Python2 bindings.

Python-pyfaidx
efficient random access to fasta subsequences for Python
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Samtools provides a function "faidx" (FAsta InDeX), which creates a small flat index file ".fai" allowing for fast random access to any subsequence in the indexed FASTA file, while loading a minimal amount of the file in to memory. This Python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script "faidx" is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge.

This package provides the Python 2 modules to access fasta files.

Please cite: Matthew D. Shirley, Zhaorong Ma, Brent S. Pedersen and Sarah J. Wheelan: Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196 (2015)
Python-pyvcf
Variant Call Format (VCF) parser for Python
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The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project.

The intent of this module is to mimic the csv module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. vcf will attempt to parse the content of each record based on the data types specified in the meta-information lines -- specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings.

This package provides the Python 2 modules.

Python-ruffus
Python computation pipeline library widely used in bioinformatics
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Ruffus is designed to allow scientific and other analyses to be automated with the minimum of fuss and the least effort.

  • Lightweight: Suitable for the simplest of tasks
  • Scalable: Handles even fiendishly complicated pipelines which would cause make or scons to go cross-eyed and recursive.
  • Standard Python: No "clever magic", no pre-processing.
  • Unintrusive: Unambitious, lightweight syntax which tries to do this one small thing well.
Please cite: Leo Goodstadt: Ruffus: A Lightweight Python Library for Computational Pipelines. (PubMed,eprint) Bioinformatics 26(21):2778-9 (2010)
Python-skbio
Python data structures, algorithms, educational resources for bioinformatics
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Scikit-bio is a Python package providing data structures, algorithms, and educational resources for bioinformatics.

This is the package for Python2

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)
R-bioc-affy
BioConductor methods for Affymetrix Oligonucleotide Arrays
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This is part of the BioConductor GNU R suite. The package contains functions for exploratory oligonucleotide array analysis.

Please cite: Laurent Gautier, Leslie Cope, Benjamin M. Bolstad and Rafael A. Irizarry: affy - analysis of Affymetrix GeneChip data at the probe level. (PubMed,eprint) Bioinformatics (3):307-315 (2004)
R-bioc-affyio
BioConductor tools for parsing Affymetrix data files
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This BioConductor package provides routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.

R-bioc-altcdfenvs
BioConductor alternative CDF environments
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This BioConductor module provides alternative CDF environments (aka probeset mappings) which are Convenience data structures and functions to handle cdfenvs.

Please cite: Laurent Gautier, Morten Mooller, Lennart Friis-Hansen and Steen Knudsen: Alternative mapping of probes to genes for Affymetrix chips. (PubMed,eprint) BMC Bioinformatics (5):111 (2004)
R-bioc-annotationdbi
GNU R Annotation Database Interface for BioConductor
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This BioConductor module provides user interface and database connection code for annotation data packages using SQLite data storage.

R-bioc-biocgenerics
generic functions for Bioconductor
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S4 generic functions needed by many other Bioconductor packages.

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

R-bioc-biomart
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
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In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

Please cite: Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber: Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. (PubMed) Nature Protocols 4(8):1184-1191 (2009)
R-bioc-biovizbase
GNU R basic graphic utilities for visualization of genomic data
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The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

R-bioc-bsgenome
BioConductor infrastructure for Biostrings-based genome data packages
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This BioConductor module provides some basic infrastructure for Biostrings-based genome data packages.

R-bioc-genomeinfodb
BioConductor utilities for manipulating chromosome identifiers
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This package contains BioConductor utilities for manipulating chromosome and other 'seqname' identifiers.

The Seqnames package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

R-bioc-genomicalignments
BioConductor representation and manipulation of short genomic alignments
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This BioConductor package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Please cite: Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan and Vincent J. Carey: Software for Computing and Annotating Genomic Ranges. (PubMed,eprint) PLoS Computational Biology 9(8):e1003118 (2013)
R-bioc-genomicfeatures
GNU R tools for making and manipulating transcript centric annotations
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A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

Please cite: M. Lawrence, W. Huber, H. Pagès, P. Aboyoun and M. Carlson et al.: Software for Computing and Annotating Genomic Ranges. (PubMed,eprint) PLoS Comput Biol 9(8):e1003118 (2013)
R-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
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The ability to efficiently store genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

R-bioc-graph
handle graph data structures for BioConductor
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This BioConductor module implements some simple graph handling capabilities. These are for instance used in hypergraph module which in turn is used by several other BioConductor packages.

R-bioc-hypergraph
BioConductor hypergraph data structures
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This package BioConductor implements some simple capabilities for representing and manipulating hypergraphs.

R-bioc-iranges
GNU R low-level containers for storing sets of integer ranges
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The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions.

R-bioc-makecdfenv
BioConductor CDF Environment Maker
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This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.

R-bioc-preprocesscore
BioConductor collection of pre-processing functions
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This BioConductor module contains a library of pre-processing functions. It is imported by several other BioConductor modules.

R-bioc-rsamtools
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
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This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

R-bioc-shortread
GNU R classes and methods for high-throughput short-read sequencing data
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This BioConductor module is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.

Please cite: Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Hervé Pagès and Robert Gentleman: ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. (PubMed,eprint) Bioinformatics 25(19):2607-2608 (2009)
R-bioc-snpstats
BioConductor SnpMatrix and XSnpMatrix classes and methods
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This BioConductor package provides R functions to work with SnpMatrix and XSnpMatrix classes and methods.

R-bioc-variantannotation
BioConductor annotation of genetic variants
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This BioConductor package provides R functions to annotate variants, compute amino acid coding changess and to predict coding outcomes.

R-bioc-xvector
BioConductor representation and manpulation of external sequences
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This BioConductor package provides memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).

R-cran-rocr
GNU R package to prepare and display ROC curves
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fieldstatistics
roleshared-lib
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ROC graphs, sensitivity/specificity curves, lift charts, and precision/recall plots are popular examples of trade-off visualizations for specific pairs of performance measures. ROCR is a flexible tool for creating cutoff-parametrized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parametrization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism. Despite its flexibility, ROCR is easy to use, with only three commands and reasonable default values for all optional parameters.

ROCR features: ROC curves, precision/recall plots, lift charts, cost curves, custom curves by freely selecting one performance measure for the x axis and one for the y axis, handling of data from cross-validation or bootstrapping, curve averaging (vertically, horizontally, or by threshold), standard error bars, box plots, curves that are color-coded by cutoff, printing threshold values on the curve, tight integration with Rs plotting facilities (making it easy to adjust plots or to combine multiple plots), fully customizable, easy to use (only 3 commands).

Performance measures that ROCR knows: Accuracy, error rate, true positive rate, false positive rate, true negative rate, false negative rate, sensitivity, specificity, recall, positive predictive value, negative predictive value, precision, fallout, miss, phi correlation coefficient, Matthews correlation coefficient, mutual information, chi square statistic, odds ratio, lift value, precision/recall F measure, ROC convex hull, area under the ROC curve, precision/recall break-even point, calibration error, mean cross-entropy, root mean squared error, SAR measure, expected cost, explicit cost.

Please cite: Tobias Sing, Oliver Sander, Niko Beerenwinkel and Thomas Lengauer: ROCR: visualizing classifier performance in R. (PubMed,eprint) Bioinformatics 21(20):3940-3941 (2005)

Debian packages in contrib or non-free

Mgltools-networkeditor
Python GUI library for the editing of networks
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This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds.

It provides a graphics user interface to edit networks and is used by the Vision packages that formulates workflows.

Mgltools-pybabel
molecular structure file access and interpretation
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This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds.

The library reimplements routines of Babel v1.6 from Pat Walters and Math Stahl in Python for reading and interpreting molecular structures. It is needed by mgltools-autodocktools at runtime.

Mgltools-vision
Python-based Visual Programming Environment
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This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds.

Vision is a visual-programming environment in which a user can interactively build networks describing novel combinations of computational methods, and yielding new visualizations of their data without actually writing code.

Debian packages in New queue (hopefully available soon)

Libgkarrays-dev
Debug symbols for libgkarrays1
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Gk-arrays are provided as a simple-to-use C++ library dedicated to queries on large collection of sequences as produced by high-throughput sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).

Gk-arrays index k-mers of reads and allows one to answer different queries on that read collection (e.g. how many reads share this k-mer? where does this k-mer occur in the read collection?).

Gk-arrays consist of a space-efficient alternative to hash tables while being similar in terms of query times.

This is the development library for libgkarrays.

Please cite: Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes and Eric Rivals: Querying large read collections in main memory: a versatile data structure. (PubMed) BMC Bioinformatics 12:242 (2011)

Packaging has started and developers might try the packaging code in VCS

Libforester-java
Libraries for evolutionary biology and comparative genomics research
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Forester is a library of Java software for phylogenomics and evolutionary biology research. It can be used to read or write phylogenetic trees, export trees to graphics file,...

Libqcpp-dev
C++11 library for NGS data quality control -- headers
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A C++ library for next-gen sequencing data quality control.

QC++ implements adaptor trimming, windowed quality trimming, length filtering and trimming, format conversion, and basic read manipulation. It also provides classes for impelementation of new measures and easy creation of bespoke filtering tools.

This package provides the development headers and static archive.

Libswarm2-dev
agent-based modeling to education, biomedical research and others
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The Swarm conceptual framework for agent-based model (ABMs) and provides many tools for implementing, observing and conducting experiments on ABMs. Users write their own software but (a) follow Swarm's conceptual framework and conventions to design the software, and (b) use the Swarm libraries to do much of the work. The library is written in Objective-C.

This package contains the development files and documentation for developing agent-based models using Swarm.

Python-intervaltree-bio
Interval tree convenience classes for genomic data -- Python 2 library
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Convenience classes for loading UCSC genomic annotation records into a set of interval tree data structures.

This package provides the Python 2 library.

Python-pyfasta
fast, memory-efficient Python 2 access to fasta sequence files
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In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a standard in the field of bioinformatics.

This package provides the Python 2 modules to access fasta files.

Remark of Debian Med team: Testsuite uncovers problems and code is not actively maintained

The upstream author of python-pyfasta confirmed that he stopped the development and recommends python-pyfaidx instead. So the packaging code for python-pyfasta in SVN works but there is no intend to really upload the package.

Python3-intervaltree-bio
Interval tree convenience classes for genomic data -- Python 3 library
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Convenience classes for loading UCSC genomic annotation records into a set of interval tree data structures.

This package provides the Python 3 library.

Python3-pyfasta
fast, memory-efficient Python 3 access to fasta sequence files
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In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a standard in the field of bioinformatics.

This package provides the Python 3 modules to access fasta files.

Remark of Debian Med team: Testsuite uncovers problems and code is not actively maintained

The upstream author of python-pyfasta confirmed that he stopped the development and recommends python-pyfaidx instead. So the packaging code for python-pyfasta in SVN works but there is no intend to really upload the package.

No known packages available but some record of interest (WNPP bug)

Libgff-perl - wnpp
Perl bindings for GFF Annotation Protocol
Responsible: David Paleino
License: GPL-1+
Debian package not available

GFF (Gene Finding Feature) is a format for describing genes and other features associated with DNA, RNA and Protein sequences.

This package provides a Perl module to use GFF objects.

No known packages available

Bioclipse
platform for chemo- and bioinformatics based on Eclipse
License: Eclipse Public License (EPL) + exception
Debian package not available

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

Bioclipse will provide functionality for chemo- and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin. To stay updated on upcoming features, releases, new plugins etc, please register for the mailing list bioclipse-announce. The development is best followed on the Bioclipse Wiki where we document the progress and ideas of the development on a daily basis.

Octace-bioinfo
Bioinformatics manipulation for Octave
License: GPL-2+
Debian package not available
 aa2int:
   Convert amino acid characters into integers.
 aminolookup:
   Convert between amino acid representations.
 cleave:
   Cleave a peptide SEQUENCE using the PATTERN at the POSITION relative to the pattern.
 int2aa
   Convert amino acid integers into characters.
 seqreverse
   Reverse a nucleotide sequence.
*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 192052