Debian Med Biology development packages

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.

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.

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.

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).

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

This package supplies development versions of NCBI's non-graphical C libraries, along with the corresponding header files.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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 TaxonomyTree project is a library used by other Ribosomal Database Project (RDP) tools.

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.

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.

'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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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".

Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic biological applications.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.