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
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Debian Med Biology development packages
Official Debian packages with high relevance
Bio-tradis
analyse the output from TraDIS analyses of genomic sequences
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Versions of package bio-tradis |
Release | Version | Architectures |
sid | 1.4.1+dfsg-1 | all |
buster | 1.4.1+dfsg-1 | all |
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License: DFSG free
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Bio-Tradis contains a set of tools to analyse the output from
TraDIS analyses.
The Bio-Tradis analysis pipeline is implemented as an extensible Perl
library which can either be used as is, or as a basis for the
development of more advanced analysis tools.
Please note: You need to manually install BioConductor Edger which can
not be distributed by Debian in recent version since it is using
non-distributable code locfit.
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Bioperl
Perl tools for computational molecular biology
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Versions of package bioperl |
Release | Version | Architectures |
sid | 1.7.4-1 | all |
squeeze | 1.6.1-2 | all |
wheezy | 1.6.901-3 | all |
jessie | 1.6.924-1 | all |
stretch | 1.7.1-2 | all |
buster | 1.7.2-3 | all |
upstream | 1.7.5 |
Debtags of package bioperl: |
devel | lang:perl, library |
field | biology, biology:bioinformatics |
role | devel-lib, shared-lib |
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License: DFSG free
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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)
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Bioperl-run
BioPerl wrappers: scripts
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Versions of package bioperl-run |
Release | Version | Architectures |
wheezy | 1.6.9-1 | all |
sid | 1.7.3-1 | all |
buster | 1.7.2-4 | all |
stretch | 1.7.1-3 | all |
squeeze | 1.6.1-1 | all |
jessie | 1.6.9-2 | all |
Debtags of package bioperl-run: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
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License: DFSG free
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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.
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Biosquid
utilities for biological sequence analysis
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Versions of package biosquid |
Release | Version | Architectures |
wheezy | 1.9g+cvs20050121-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
squeeze | 1.9g+cvs20050121-2 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
sid | 1.9g+cvs20050121-11 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.9g+cvs20050121-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.9g+cvs20050121-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.9g+cvs20050121-4 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package biosquid: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing, converting, editing |
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License: DFSG free
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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.
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Cwltool
Common Workflow Language reference implementation
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Versions of package cwltool |
Release | Version | Architectures |
buster | 1.0.20181217162649+dfsg-10 | all |
stretch | 1.0.20170114120503-1 | all |
sid | 1.0.20181217162649+dfsg-10 | all |
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License: DFSG free
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This is the reference implementation of the Common Workflow Language
standards.
The CWL open standards are for describing analysis workflows and tools in a
way that makes them portable and scalable across a variety of software and
hardware environments, from workstations to cluster, cloud, and high
performance computing (HPC) environments. CWL is designed to meet the needs of
data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy,
Physics, and Chemistry.
The CWL reference implementation (cwltool) is intended to be feature complete
and to provide comprehensive validation of CWL files as well as provide other
tools related to working with CWL descriptions.
Please cite:
Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić, Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes and Luka Stojanovic:
Common Workflow Language, v1.0.
(2016)
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Libace-perl
Object-Oriented Access to ACEDB Databases
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Versions of package libace-perl |
Release | Version | Architectures |
wheezy | 1.92-2 | amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc |
squeeze | 1.92-2 | amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc |
sid | 1.92-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.92-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.92-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.92-3 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package libace-perl: |
devel | lang:perl, library |
field | biology |
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License: DFSG free
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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).
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Libai-fann-perl
Perl wrapper for the FANN library
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Versions of package libai-fann-perl |
Release | Version | Architectures |
stretch | 0.10-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.10-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 0.10-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.10-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 0.10-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
Debtags of package libai-fann-perl: |
devel | lang:perl, library |
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License: DFSG free
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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.
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Libbambamc-dev
Development files for reading and writing BAM (genome alignment) files
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Versions of package libbambamc-dev |
Release | Version | Architectures |
stretch | 0.0.50-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.0.50-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.0.50-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.0.50-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
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License: DFSG free
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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.
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Libbamtools-dev
C++ API for manipulating BAM (genome alignment) files
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Versions of package libbamtools-dev |
Release | Version | Architectures |
sid | 2.5.1+dfsg-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.3.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 2.4.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.5.1+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Libbio-asn1-entrezgene-perl
parser for NCBI Entrez Gene and NCBI Sequence records
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Versions of package libbio-asn1-entrezgene-perl |
Release | Version | Architectures |
buster | 1.720-2 | all |
stretch | 1.720-1 | all |
squeeze | 1.091-2 | all |
wheezy | 1.100-1 | all |
sid | 1.720-2 | all |
jessie | 1.700-1 | all |
upstream | 1.730 |
Debtags of package libbio-asn1-entrezgene-perl: |
devel | lang:perl |
field | biology |
works-with-format | plaintext |
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License: DFSG free
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Bio::ASN1::EntrezGene and Bio::ASN1::Sequence are regular expression-based
parsers for NCBI Entrez Gene genome databases
(http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene).
They parse ASN.1-formatted Entrez Gene records and NCBI sequences,
returning data structures that contain all data items from the gene records
or the sequence records.
The parser will report error & line number if input data does not conform to
the NCBI Entrez Gene genome or NCBI Sequence annotation file format.
Bio::ASN1::Sequence is basically a modified version of the high-performance
Bio::ASN1::EntrezGene parser. However this standalone module exists since it
is more efficient to keep Sequence-specific code out of EntrezGene.pm.
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Libbio-chado-schema-perl
DBIx::Class layer for the Chado database schema
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Versions of package libbio-chado-schema-perl |
Release | Version | Architectures |
wheezy | 0.10010-1 | all |
sid | 0.20000-2 | all |
buster | 0.20000-2 | all |
stretch | 0.20000-1 | all |
jessie | 0.20000-1 | all |
Debtags of package libbio-chado-schema-perl: |
devel | lang:perl, library |
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License: DFSG free
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The module Bio::Chado::Schema is a standard object-relational mapping
layer for use with the GMOD Chado database schema.
Chado is an open-source modular database schema for biological data.
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Libbio-coordinate-perl
BioPerl modules for working with biological coordinates
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Versions of package libbio-coordinate-perl |
Release | Version | Architectures |
buster | 1.7.1-3 | all |
sid | 1.7.1-3 | all |
stretch | 1.7.1-1 | all |
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License: DFSG free
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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.
Since BioPerl version 1.7 several modules where split into separate projects.
This package provides the Bio::Coordinate module for working with biological
coordinates.
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Libbio-das-lite-perl
implementation of the BioDas protocol
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Versions of package libbio-das-lite-perl |
Release | Version | Architectures |
buster | 2.11-7 | all |
wheezy | 2.04-1.1 | all |
jessie | 2.04-1.1 | all |
sid | 2.11-7 | all |
stretch | 2.11-5 | all |
Debtags of package libbio-das-lite-perl: |
devel | lang:perl, library |
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License: DFSG free
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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.
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Libbio-eutilities-perl
BioPerl interface to the Entrez Programming Utilities (E-utilities)
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Versions of package libbio-eutilities-perl |
Release | Version | Architectures |
sid | 1.75-4 | all |
buster | 1.75-4 | all |
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License: DFSG free
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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. This
package provides a programmatic interface to NCBI's Entrez Programming
Utilities commonly referred to as E-utilities. Namely, it provides the
Bio::DB::EUtilities and Bio::Tools::EUtilities perl modules.
Entrez is a federated search engine at the National Center for
Biotechnology Information (NCBI) for a large number of databases
covering a variety of biomedical data, including nucleotide and
protein sequences, gene records, three-dimensional molecular
structures, and the biomedical literature. E-utilities are a set of
eight server-side programs that provide a stable interface into the
Entrez query and database system at the National Center for
Biotechnology Information (NCBI).
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Libbio-graphics-perl
Generate GD images of Bio::Seq objects
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Versions of package libbio-graphics-perl |
Release | Version | Architectures |
squeeze | 2.11-1 | all |
sid | 2.40-3 | all |
buster | 2.40-3 | all |
stretch | 2.40-1 | all |
jessie | 2.39-2 | all |
wheezy | 2.26-1 | all |
Debtags of package libbio-graphics-perl: |
devel | lang:perl, library |
field | biology, biology:bioinformatics |
role | shared-lib |
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License: DFSG free
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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.
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Libbio-mage-perl
Container module for classes in the MAGE package: MAGE
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Versions of package libbio-mage-perl |
Release | Version | Architectures |
wheezy | 20030502.3-2 | all |
buster | 20030502.3-5 | all |
stretch | 20030502.3-3 | all |
jessie | 20030502.3-3 | all |
sid | 20030502.3-5 | all |
squeeze | 20030502.3-2 | all |
Debtags of package libbio-mage-perl: |
field | biology, biology:bioinformatics |
role | devel-lib |
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License: DFSG free
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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
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Libbio-mage-utils-perl
Extra modules for classes in the MAGE package: MAGE
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Versions of package libbio-mage-utils-perl |
Release | Version | Architectures |
buster | 20030502.0-4 | all |
wheezy | 20030502.0-1 | all |
squeeze | 20030502.0-1 | all |
stretch | 20030502.0-2 | all |
jessie | 20030502.0-2 | all |
sid | 20030502.0-4 | all |
Debtags of package libbio-mage-utils-perl: |
field | biology, biology:bioinformatics |
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License: DFSG free
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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.
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Libbio-primerdesigner-perl
Perl module to design PCR primers using primer3 and epcr
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Versions of package libbio-primerdesigner-perl |
Release | Version | Architectures |
sid | 0.07-6 | all |
squeeze | 0.07-1 | all |
wheezy | 0.07-1 | all |
jessie | 0.07-3 | all |
stretch | 0.07-5 | all |
buster | 0.07-6 | all |
Debtags of package libbio-primerdesigner-perl: |
devel | lang:perl, library |
role | shared-lib |
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License: DFSG free
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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.
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Libbio-samtools-perl
Perl interface to SamTools library for DNA sequencing
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Versions of package libbio-samtools-perl |
Release | Version | Architectures |
buster | 1.43-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.43-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.39-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 1.33-1 | amd64,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390 |
squeeze | 1.20-1 | amd64,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390 |
sid | 1.43-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbio-samtools-perl: |
devel | lang:perl, library |
role | shared-lib |
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License: DFSG free
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Bio::SamTools provides a Perl interface to the libbam library for indexed and
unindexed SAM/BAM sequence alignment databases. It provides support for
retrieving information on individual alignments, read pairs, and alignment
coverage information across large regions. It also provides callback
functionality for calling SNPs and performing other base-by-base functions.
Most operations are compatible with the BioPerl Bio::SeqFeatureI interface,
allowing BAM files to be used as a backend to the GBrowse genome browser
application.
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Libbio-scf-perl
Perl extension for reading and writing SCF sequence files
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Versions of package libbio-scf-perl |
Release | Version | Architectures |
jessie | 1.03-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc |
stretch | 1.03-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.03-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 1.03-1 | amd64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,sparc |
squeeze | 1.03-1 | amd64,i386 |
sid | 1.03-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbio-scf-perl: |
devel | lang:perl, library |
role | shared-lib |
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License: DFSG free
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The Bio::SCF (Standard Chromatogram Format) module allows you to read and
update (in a restricted way) SCF chromatographic sequence files. It is an
interface to Roger Staden's io-lib. It has both tied hash and an
object-oriented interfaces. It provides the ability to read fields from SCF
files and limited ability to modify them and write them back.
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Libbio-tools-phylo-paml-perl
Bioperl interface to the PAML suite
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Versions of package libbio-tools-phylo-paml-perl |
Release | Version | Architectures |
buster | 1.7.3-2 | all |
sid | 1.7.3-2 | all |
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License: DFSG free
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This distribution provides a Perl interface to PAML, a suite of
programs (baseml, codeml, evolver, and yn00) for phylogenetic
analyses of DNA or protein sequences using maximum likelihood.
The Bio::Tools::Run::Phylo::PAML::* modules provide an interface to
run the PAML programs while Bio::Tools::Phylo::PAML provides an
interface to parse their output files.
This distribution is part of the Bioperl project.
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Libbio-tools-run-alignment-clustalw-perl
Bioperl interface to Clustal W
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Versions of package libbio-tools-run-alignment-clustalw-perl |
Release | Version | Architectures |
sid | 1.7.4-1 | all |
buster | 1.7.4-1 | all |
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License: DFSG free
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Bio::Tools::Run::Alignment::Clustalw provides a Perl interface to
Clustal W, a program for alignment of multiple nucleotide and peptide
sequences.
This module distribution is part of the Bioperl project.
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Libbio-tools-run-alignment-tcoffee-perl
Bioperl interface to T-Coffee
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Versions of package libbio-tools-run-alignment-tcoffee-perl |
Release | Version | Architectures |
buster | 1.7.4-1 | all |
sid | 1.7.4-1 | all |
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License: DFSG free
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Bio::Tools::Run::Alignment::TCoffee provides a Perl interface to
T-Coffee, a program for multiple alignments of DNA, RNA, and protein
sequences and structures.
This module distribution is part of the Bioperl project.
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Libbiococoa-dev
Bioinformatics framework for GNUstep and Cocoa (development files)
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Versions of package libbiococoa-dev |
Release | Version | Architectures |
buster | 2.2.2-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.2.2-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.2-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 2.2.2-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
Debtags of package libbiococoa-dev: |
biology | nuceleic-acids, peptidic |
devel | library |
field | biology, biology:bioinformatics |
role | devel-lib, shared-lib |
suite | gnustep |
uitoolkit | gnustep |
|
License: DFSG free
|
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.
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|
Libbiod-dev
bioinformatics library in D (development files)
|
Versions of package libbiod-dev |
Release | Version | Architectures |
sid | 0.1.0-6 | i386 |
sid | 0.2.1-1 | amd64 |
buster | 0.1.0-6 | amd64,i386 |
|
License: DFSG free
|
BioD is a fast and memory efficient bioinformatics library written in
the D programming language. BioD aims to:
- Provide a platform for writing high-performance bioinformatics
applications in D. BioD achieves this by:
- automatic parallelization of tasks where possible for example
reading and writing BAM files.
- reducing the GC overhead by avoiding unnecessary memory allocations
- Offer support for manipulating common biological data formats.
- Write clear documented and maintainable codebase.
This package contains the include files for development.
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|
Libbiojava-java
Java API to biological data and applications (default version)
|
Versions of package libbiojava-java |
Release | Version | Architectures |
squeeze | 1.7.1-1 | all |
wheezy | 1.7.1-2 | all |
buster | 1.7.1-8 | all |
sid | 1.7.1-8 | all |
stretch | 1.7.1-5 | all |
jessie | 1.7.1-5 | all |
upstream | 1.9.3 |
Debtags of package libbiojava-java: |
devel | lang:java, library |
field | biology, biology:bioinformatics |
role | devel-lib |
|
License: DFSG free
|
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.
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Libbiojava4-java
Java API to biological data and applications (default version)
|
Versions of package libbiojava4-java |
Release | Version | Architectures |
sid | 4.2.12+dfsg-2 | all |
buster | 4.2.12+dfsg-2 | all |
stretch | 4.2.5+dfsg-1 | all |
|
License: DFSG free
|
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.
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|
Libbioparser-dev
library for parsing several formats in bioinformatics
|
Versions of package libbioparser-dev |
Release | Version | Architectures |
buster | 1.2.1-1 | all |
sid | 1.2.1-1 | all |
|
License: DFSG free
|
Bioparser is a c++ implementation of parsers for several bioinformatics
formats. It consists of only one header file containing template parsers
for FASTA, FASTQ, MHAP, PAF and SAM format. It also supports compressed
files with gzip.
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|
Libblasr-dev
tools for aligning PacBio reads to target sequences (development files)
|
Versions of package libblasr-dev |
Release | Version | Architectures |
buster | 5.3.1+dfsg-2.1 | amd64,arm64,mips64el,ppc64el |
sid | 5.3.1+dfsg-2.1 | amd64,arm64,mips64el,ppc64el |
sid | 0~20160705-1 | hurd-i386 |
stretch | 0~20161219-1 | amd64,arm64,mips64el,ppc64el |
sid | 5.3.1+dfsg-2 | kfreebsd-amd64 |
|
License: DFSG free
|
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.
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Libbpp-core-dev
Bio++ Core library development files
|
Versions of package libbpp-core-dev |
Release | Version | Architectures |
buster | 2.4.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.0-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 2.0.3-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
Debtags of package libbpp-core-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libbpp-phyl-dev
Bio++ Phylogenetic library development files
|
Versions of package libbpp-phyl-dev |
Release | Version | Architectures |
stretch | 2.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 2.4.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 2.0.3-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
Debtags of package libbpp-phyl-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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 for phylogenetics.
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Libbpp-phyl-omics-dev
Bio++ Phylogenetics library: genomics components (development files)
|
Versions of package libbpp-phyl-omics-dev |
Release | Version | Architectures |
sid | 2.4.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 2.4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbpp-phyl-omics-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libbpp-popgen-dev
Bio++ Population Genetics library development files
|
Versions of package libbpp-popgen-dev |
Release | Version | Architectures |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 2.0.3-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
buster | 2.4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbpp-popgen-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libbpp-qt-dev
Bio++ Qt Graphic classes library development files
|
Versions of package libbpp-qt-dev |
Release | Version | Architectures |
buster | 2.4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 2.0.2-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
stretch | 2.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 2.4.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbpp-qt-dev: |
devel | library |
role | devel-lib |
uitoolkit | qt |
|
License: DFSG free
|
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.
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Libbpp-raa-dev
Bio++ Remote Acnuc Access library development files
|
Versions of package libbpp-raa-dev |
Release | Version | Architectures |
stretch | 2.2.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 2.0.3-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
buster | 2.4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbpp-raa-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libbpp-seq-dev
Bio++ Sequence library development files
|
Versions of package libbpp-seq-dev |
Release | Version | Architectures |
buster | 2.4.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 2.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 2.0.3-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 2.4.1-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbpp-seq-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libbpp-seq-omics-dev
Bio++ Sequence library: genomics components (development files)
|
Versions of package libbpp-seq-omics-dev |
Release | Version | Architectures |
sid | 2.4.1-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 2.4.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.2.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbpp-seq-omics-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libchado-perl
database schema and tools for genomic data
|
Versions of package libchado-perl |
Release | Version | Architectures |
buster | 1.31-5 | all |
stretch | 1.31-3 | all |
jessie | 1.23-2 | all |
wheezy | 1.22-4 | all |
sid | 1.31-5 | all |
Debtags of package libchado-perl: |
devel | lang:perl, library |
|
License: DFSG free
|
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.
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Libconsensuscore-dev
algorithms for PacBio multiple sequence consensus -- development files
|
Versions of package libconsensuscore-dev |
Release | Version | Architectures |
buster | 1.1.1+dfsg-1 | amd64,i386 |
sid | 1.1.1+dfsg-1 | amd64,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386 |
stretch | 1.0.2-2 | amd64,i386 |
|
License: DFSG free
|
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.
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Libdivsufsort-dev
libdivsufsort header files
|
Versions of package libdivsufsort-dev |
Release | Version | Architectures |
buster | 2.0.1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.0.1-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.0.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Libedlib-dev
library for sequence alignment using edit distance (devel)
|
Versions of package libedlib-dev |
Release | Version | Architectures |
buster | 1.2.4-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.3-3 | kfreebsd-i386 |
sid | 1.2.4-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
A lightweight and super fast C/C++ library for sequence alignment using
edit distance.
Calculating edit distance of two strings is as simple as:
edlibAlign("hello", 5, "world!", 6,
edlibDefaultAlignConfig()).editDistance;
Features
- Calculates edit distance (Levehnstein distance).
- It can find optimal alignment path (instructions how to transform
first sequence into the second sequence).
- It can find just the start and/or end locations of alignment path -
can be useful when speed is more important than having exact
alignment path.
- Supports multiple alignment methods: global(NW), prefix(SHW) and
infix(HW), each of them useful for different scenarios.
- You can extend character equality definition, enabling you to e.g.
have wildcard characters, to have case insensitive alignment or to
work with degenerate nucleotides.
- It can easily handle small or very large sequences, even when finding
alignment path, while consuming very little memory.
- Super fast thanks to Myers's bit-vector algorithm.
This package contains the static library and the header files.
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Libfast5-dev
library for reading Oxford Nanopore Fast5 files -- headers
|
Versions of package libfast5-dev |
Release | Version | Architectures |
stretch | 0.5.8-1 | all |
sid | 0.6.5-2 | all |
buster | 0.6.5-2 | all |
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License: DFSG free
|
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.
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Libfastahack-dev
library for indexing and sequence extraction from FASTA files (devel)
|
Versions of package libfastahack-dev |
Release | Version | Architectures |
sid | 0.0+git20160702.bbc645f+dfsg-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.0+20160702-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el |
buster | 0.0+git20160702.bbc645f+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
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Libffindex0-dev
library for simple index/database for huge amounts of small files (development)
|
Versions of package libffindex0-dev |
Release | Version | Architectures |
buster | 0.9.9.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.9.9.7-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.9.9.3-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 0.9.6.1-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 0.9.9.9-1 | amd64,arm64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libffindex0-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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Libfml-dev
development headers for libfml
|
Versions of package libfml-dev |
Release | Version | Architectures |
buster | 0.1-5 | amd64 |
stretch | 0.1-2 | amd64 |
sid | 0.1-5 | amd64,kfreebsd-amd64 |
|
License: DFSG free
|
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.
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Libfreecontact-dev
fast protein contact predictor library - development files
|
Versions of package libfreecontact-dev |
Release | Version | Architectures |
sid | 1.0.21-7 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.21-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.21-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
|
|
Libfreecontact-perl
fast protein contact predictor - binding for Perl
|
Versions of package libfreecontact-perl |
Release | Version | Architectures |
jessie | 0.08-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 0.08-7 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.08-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.08-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libfreecontact-perl: |
devel | lang:perl, library |
|
License: DFSG free
|
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.
|
|
Libgatbcore-dev
development library of the Genome Analysis Toolbox
|
Versions of package libgatbcore-dev |
Release | Version | Architectures |
buster | 1.4.1+git20181225.44d5a44+dfsg-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
sid | 1.4.1+git20181225.44d5a44+dfsg-1 | amd64,arm64,i386,mips64el,ppc64el,s390x |
upstream | 1.4.1+git20190126.0a106c4 |
|
License: DFSG free
|
The GATB-CORE project provides a set of highly efficient
algorithms to analyse NGS data sets. These methods enable
the analysis of data sets of any size on multi-core desktop
computers, including very huge amount of reads data coming
from any kind of organisms such as bacteria, plants,
animals and even complex samples (e.g. metagenomes).
Read more about GATB at https://gatb.inria.fr/.
By itself GATB-CORE is not an NGS data analysis tool.
However, it can be used to create such tools. There already
exist a set of ready-to-use tools relying on GATB-CORE
library: see https://gatb.inria.fr/software/
This package contains the static library and the header files
of the gatb-core library.
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|
Libgenome-dev
toolkit for developing bioinformatic related software (devel)
|
Versions of package libgenome-dev |
Release | Version | Architectures |
buster | 1.3.11+svn20110227.4616-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.3.11+svn20110227.4616-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
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|
Libgenome-model-tools-music-perl
module for finding mutations of significance in cancer
|
Versions of package libgenome-model-tools-music-perl |
Release | Version | Architectures |
stretch | 0.04-3 | all |
jessie | 0.04-1 | all |
buster | 0.04-4 | all |
sid | 0.04-4 | all |
Debtags of package libgenome-model-tools-music-perl: |
devel | lang:perl, library |
|
License: DFSG free
|
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
|
Versions of package libgenome-perl |
Release | Version | Architectures |
stretch | 0.06-3 | all |
jessie | 0.06-1 | all |
buster | 0.06-5 | all |
sid | 0.06-5 | all |
Debtags of package libgenome-perl: |
devel | lang:perl, library |
|
License: DFSG free
|
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.
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|
Libgenometools0-dev
development files for GenomeTools
|
Versions of package libgenometools0-dev |
Release | Version | Architectures |
buster | 1.5.10+ds-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.5.9+ds-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.3-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.5.10+ds-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libgenometools0-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
|
|
Libgff-dev
GFF/GTF parsing from cufflinks as a library
|
Versions of package libgff-dev |
Release | Version | Architectures |
sid | 1.0-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Libgkarrays-dev
library to query large collection of NGS sequences (development)
|
Versions of package libgkarrays-dev |
Release | Version | Architectures |
buster | 2.1.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.0+dfsg-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.1.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Libgo-perl
perl modules for GO and other OBO ontologies
|
Versions of package libgo-perl |
Release | Version | Architectures |
sid | 0.15-7 | all |
jessie | 0.15-1 | all |
squeeze | 0.12-1 | all |
wheezy | 0.13-3 | all |
stretch | 0.15-5 | all |
buster | 0.15-7 | all |
Debtags of package libgo-perl: |
field | biology, biology:bioinformatics |
interface | commandline |
role | devel-lib, program |
scope | utility |
use | analysing, converting |
works-with-format | plaintext, xml |
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License: DFSG free
|
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.
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|
Libhmsbeagle-dev
High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
|
Versions of package libhmsbeagle-dev |
Release | Version | Architectures |
jessie | 2.1.2-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 3.1.2+dfsg-3 | amd64,arm64,armhf,i386 |
buster | 3.1.2+dfsg-3 | amd64,arm64,armhf,i386 |
wheezy | 1.0-6 | amd64,armel,armhf,i386,ia64,mips,mipsel,powerpc,s390,s390x,sparc |
stretch | 2.1.2+20160831-5 | amd64,arm64,armhf,i386 |
Debtags of package libhmsbeagle-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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)
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|
Libhts-dev
development files for the HTSlib
|
Versions of package libhts-dev |
Release | Version | Architectures |
jessie | 1.1-1 | amd64,arm64,armel,i386,mipsel,ppc64el |
buster | 1.9-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.9-10 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.3.2-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
Debtags of package libhts-dev: |
devel | library |
role | devel-lib |
|
License: DFSG free
|
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.
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|
Libhtsjdk-java
Java API for high-throughput sequencing data (HTS) formats
|
Versions of package libhtsjdk-java |
Release | Version | Architectures |
buster | 2.18.2+dfsg-1 | all |
stretch | 2.8.1+dfsg-1 | all |
sid | 2.18.2+dfsg-1 | all |
|
License: DFSG free
|
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.
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Libjebl2-java
Java Evolutionary Biology Library
|
Versions of package libjebl2-java |
Release | Version | Architectures |
buster | 0.1+git20180418.653eb83-1 | all |
sid | 0.1+git20180418.653eb83-1 | all |
stretch | 0.1+20140614-1 | all |
jessie | 0.0.r22-1 | all |
wheezy | 0.0.r6-1 | all |
upstream | 0.1+git20190131.e2a7c99 |
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License: DFSG free
|
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.
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Libjloda-java
Java library of data structures and algorithms for bioinformatics
|
Versions of package libjloda-java |
Release | Version | Architectures |
buster | 0.0+git20180523.cbaf6d1-1 | all |
sid | 0.0+git20180523.cbaf6d1-1 | all |
stretch | 0.0+20161018-1 | all |
upstream | 0.0+git20190109.d96d355 |
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License: DFSG free
|
The jloda Java library provides some basic data structures and
algorithms used by bioinformatics applications like SplitsTree,
Dendroscope and MEGAN.
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|
Libkmer-dev
suite of tools for DNA sequence analysis (development lib)
|
Versions of package libkmer-dev |
Release | Version | Architectures |
buster | 0~20150903+r2013-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0~20150903+r2013-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0~20150903+r2013-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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 package contains headers and static libraries for kmer.
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Libmems-dev
development library to support DNA string matching and comparative genomics
|
Versions of package libmems-dev |
Release | Version | Architectures |
sid | 1.6.0+4725-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.6.0+4725-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Libminimap-dev
development headers for libminimap
|
Versions of package libminimap-dev |
Release | Version | Architectures |
stretch | 0.2-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.2-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.2-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
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Libmuscle-dev
multiple alignment development library for protein sequences
|
Versions of package libmuscle-dev |
Release | Version | Architectures |
buster | 3.7+4565-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 3.7+4565-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Libncbi-vdb-dev
libraries for using data in the INSDC Sequence Read Archives (devel)
|
Versions of package libncbi-vdb-dev |
Release | Version | Architectures |
stretch | 2.8.1+dfsg-2 | amd64,i386 |
sid | 2.9.3+dfsg-2 | amd64,i386 |
buster | 2.9.3+dfsg-2 | amd64,i386 |
upstream | 2.9.4 |
|
License: DFSG free
|
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.
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Libncbi6-dev
NCBI libraries for biology applications (development files)
|
Versions of package libncbi6-dev |
Release | Version | Architectures |
wheezy | 6.1.20120620-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
buster | 6.1.20170106-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 6.1.20170106-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 6.1.20120620-8 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
squeeze | 6.1.20090809-2 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
sid | 6.1.20170106-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libncbi6-dev: |
biology | nuceleic-acids, peptidic |
devel | lang:c, library |
field | biology, biology:bioinformatics |
role | devel-lib |
science | calculation |
use | analysing, calculating, converting, searching |
works-with | biological-sequence |
works-with-format | plaintext, xml |
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License: DFSG free
|
This package supplies development versions of NCBI's non-graphical C
libraries, along with the corresponding header files.
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|
Libncl-dev
NEXUS Class Library (static lib and header files)
|
Versions of package libncl-dev |
Release | Version | Architectures |
buster | 2.1.21+git20180827.c71b264-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.1.18+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.1.21+git20180827.c71b264-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Libngs-java
Next Generation Sequencing language Bindings (Java bindings)
|
Versions of package libngs-java |
Release | Version | Architectures |
stretch | 1.3.0-2 | amd64,i386 |
sid | 2.9.3-1 | amd64,i386 |
buster | 2.9.3-1 | amd64,i386 |
upstream | 2.9.4 |
|
License: DFSG free
|
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.
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Libngs-sdk-dev
Next Generation Sequencing language Bindings (development)
|
Versions of package libngs-sdk-dev |
Release | Version | Architectures |
buster | 2.9.3-1 | amd64,i386 |
sid | 2.9.3-1 | amd64,i386 |
stretch | 1.3.0-2 | amd64,i386 |
upstream | 2.9.4 |
|
License: DFSG free
|
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.
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Libnhgri-blastall-perl
Perl extension for running and parsing NCBI's BLAST 2.x
|
Versions of package libnhgri-blastall-perl |
Release | Version | Architectures |
jessie | 0.66-1 | all |
sid | 0.66-3 | all |
buster | 0.66-3 | all |
stretch | 0.66-2 | all |
Debtags of package libnhgri-blastall-perl: |
devel | lang:perl, library |
|
License: DFSG free
|
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
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Libopenms-dev
library for LC/MS data management and analysis - dev files
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Versions of package libopenms-dev |
Release | Version | Architectures |
buster | 2.4.0-real-1 | amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.0-real-1 | amd64,arm64,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.11.1-5 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
upstream | 2.4.0-src |
Debtags of package libopenms-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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)
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Libpal-java
Phylogenetic Analysis Library
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Versions of package libpal-java |
Release | Version | Architectures |
buster | 1.5.1+dfsg-5 | all |
wheezy | 1.5.1-2 | all |
sid | 1.5.1+dfsg-5 | all |
jessie | 1.5.1-2 | all |
stretch | 1.5.1+dfsg-2 | all |
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License: DFSG free
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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.
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Libpbbam-dev
Pacific Biosciences binary alignment/map (BAM) library (headers)
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Versions of package libpbbam-dev |
Release | Version | Architectures |
buster | 0.19.0+dfsg-4 | amd64,arm64,mips64el,ppc64el |
stretch | 0.7.4+ds-1 | amd64,arm64,mips64el,ppc64el |
sid | 0.7.4+ds-1 | kfreebsd-amd64 |
sid | 0.19.0+dfsg-4 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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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.
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Libpbdata-dev
tools for handling PacBio sequences (development files)
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Versions of package libpbdata-dev |
Release | Version | Architectures |
sid | 0~20160705-1 | hurd-i386,kfreebsd-i386 |
sid | 5.3.1+dfsg-2 | kfreebsd-amd64 |
buster | 5.3.1+dfsg-2.1 | amd64,arm64,mips64el,ppc64el |
sid | 5.3.1+dfsg-2.1 | amd64,arm64,mips64el,ppc64el |
stretch | 0~20161219-1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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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.
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Libpbihdf-dev
tools for handling PacBio hdf5 files (development files)
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Versions of package libpbihdf-dev |
Release | Version | Architectures |
sid | 5.3.1+dfsg-2.1 | amd64,arm64,mips64el,ppc64el |
sid | 0~20160705-1 | hurd-i386 |
sid | 5.3.1+dfsg-2 | kfreebsd-amd64 |
buster | 5.3.1+dfsg-2.1 | amd64,arm64,mips64el,ppc64el |
stretch | 0~20161219-1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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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.
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Libpbseq-dev
library for analyzing PacBio sequencing data (development files)
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Versions of package libpbseq-dev |
Release | Version | Architectures |
sid | 5.3.1+dfsg-2 | all |
sid | 5.3.1+dfsg-2.1 | all |
stretch | 0~20161219-1 | all |
buster | 5.3.1+dfsg-2.1 | all |
sid | 0~20160705-1 | all |
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License: DFSG free
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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.
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Libpll-dev
Phylogenetic Likelihood Library (development)
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Versions of package libpll-dev |
Release | Version | Architectures |
sid | 0.3.2-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.3.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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PLL is a highly optimized, parallelized software library to ease the
development of new software tools dealing with phylogenetic inference.
Among the functions included in PLL are parsing multiple sequence
alignments (MSA) from PHYLIP and FASTA files, reading Newick trees,
performing topological moves such as SPR and NNI, model optimization,
likelihood evaluation and partitioned analysis by assigning different
substitution models to each partition of the MSA. PLL fully implements
the GTR nucleotide substitution model for DNA data and a number of
models for aminoacid data.
This package contains the static library and the header file.
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Libqes-dev
DNA sequence parsing library -- development
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Versions of package libqes-dev |
Release | Version | Architectures |
sid | 0.2.8-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.2.7-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.2.8-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Librcsb-core-wrapper0-dev
development files for librcsb-core-wrapper0
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Versions of package librcsb-core-wrapper0-dev |
Release | Version | Architectures |
sid | 1.005-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.005-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.005-3 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 1.005-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package librcsb-core-wrapper0-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Librdp-taxonomy-tree-java
taxonomy tree library from Ribosomal Database Project (RDP)
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Versions of package librdp-taxonomy-tree-java |
Release | Version | Architectures |
stretch | 1.2.0-1 | all |
buster | 1.2.0-3 | all |
sid | 1.2.0-3 | all |
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License: DFSG free
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The TaxonomyTree project is a library used by other Ribosomal Database
Project (RDP) tools.
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Librelion-dev
C++ API for RELION (3D reconstructions in cryo-electron microscopy)
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Versions of package librelion-dev |
Release | Version | Architectures |
jessie | 1.3+dfsg-2 | amd64,i386 |
buster | 1.4+dfsg-4 | amd64,i386 |
sid | 1.4+dfsg-4 | amd64,i386 |
stretch | 1.4+dfsg-2 | amd64,i386 |
upstream | 3.0 |
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License: DFSG free
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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.
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Librg-blast-parser-perl
very fast NCBI BLAST parser - binding for Perl
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Versions of package librg-blast-parser-perl |
Release | Version | Architectures |
wheezy | 0.02-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 0.03-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 0.03-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.03-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.03-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package librg-blast-parser-perl: |
devel | lang:perl, library |
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License: DFSG free
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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.
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Librg-reprof-bundle-perl
protein secondary structure and accessibility predictor (perl module)
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Versions of package librg-reprof-bundle-perl |
Release | Version | Architectures |
sid | 1.0.1-6 | all |
buster | 1.0.1-6 | all |
stretch | 1.0.1-4 | all |
jessie | 1.0.1-1 | all |
wheezy | 1.0.1-1 | all |
Debtags of package librg-reprof-bundle-perl: |
devel | lang:perl, library |
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License: DFSG free
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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.
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Librostlab-blast0-dev
very fast C++ library for parsing the output of NCBI BLAST programs (devel)
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Versions of package librostlab-blast0-dev |
Release | Version | Architectures |
wheezy | 1.0.0-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 1.0.1-9 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.1-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.1-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.1-3 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package librostlab-blast0-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Librostlab3-dev
C++ library for computational biology (development)
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Versions of package librostlab3-dev |
Release | Version | Architectures |
sid | 1.0.20-8 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.20-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.20-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.20-4 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 1.0.20-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
Debtags of package librostlab3-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Libsbml5-dev
System Biology Markup Language library - development files
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Versions of package libsbml5-dev |
Release | Version | Architectures |
jessie | 5.10.0+dfsg-1 | amd64,armel,armhf,i386,s390x |
sid | 5.17.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el |
buster | 5.17.2+dfsg-3 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el |
sid | 5.15.2+dfsg-1 | kfreebsd-amd64,kfreebsd-i386 |
stretch | 5.13.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el,s390x |
Debtags of package libsbml5-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Libseqlib-dev
C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
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Versions of package libseqlib-dev |
Release | Version | Architectures |
buster | 1.1.2+dfsg-2 | amd64 |
sid | 1.1.2+dfsg-2 | amd64,kfreebsd-amd64 |
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License: DFSG free
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C++ API and command line tool that provides a rapid and user-friendly
interface to BAM/SAM/CRAM files, global sequence alignment operations
and sequence assembly. Four C libraries perform core operations in
SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment
and Fermi for error correction and sequence assembly. Benchmarking
indicates that SeqLib has lower CPU and memory requirements than leading
C++ sequence analysis APIs. Minimal SeqLib code can extract, error-correct
and assemble reads from a CRAM file and then align with BWA-MEM.
SeqLib also provides additional capabilities, including chromosome-aware
interval queries and read plotting. Command line tools are available for
performing integrated error correction, micro-assemblies and alignment.
This package contains the header files and static library.
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Libsmithwaterman-dev
determine similar regions between two strings or genomic sequences (devel)
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Versions of package libsmithwaterman-dev |
Release | Version | Architectures |
stretch | 0.0+20160702-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el |
buster | 0.0+git20160702.2610e25-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.0+git20160702.2610e25-7 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Libsnp-sites1-dev
Static libraries and header files for the package snp-sites
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Versions of package libsnp-sites1-dev |
Release | Version | Architectures |
stretch | 2.3.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 2.4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libsnp-sites1-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Libsort-key-top-perl
Perl module to select and sort top n elements of a list
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Versions of package libsort-key-top-perl |
Release | Version | Architectures |
stretch | 0.08-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 0.06-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 0.08-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.08-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.08-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package libsort-key-top-perl: |
devel | lang:perl, library |
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License: DFSG free
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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.
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Libspoa-dev
SIMD partial order alignment library (development files)
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Versions of package libspoa-dev |
Release | Version | Architectures |
buster | 1.1.5-1 | amd64 |
sid | 1.1.5-1 | amd64 |
upstream | 2.0.0 |
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License: DFSG free
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Spoa (SIMD POA) is a c++ implementation of the partial order alignment
(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
is used to generate consensus sequences (as described in
10.1093/bioinformatics/btg109). It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
(overlap).
This package contains the static library and the header files.
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Libsrf-dev
C++ implementation of the SRF format for DNA sequence data
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Versions of package libsrf-dev |
Release | Version | Architectures |
wheezy | 0.1+dfsg-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
stretch | 0.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.1+dfsg-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.1+dfsg-4 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
squeeze | 0.1+dfsg-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
Debtags of package libsrf-dev: |
devel | library |
role | shared-lib |
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License: DFSG free
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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.
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Libssm-dev
macromolecular superposition library - development files
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Versions of package libssm-dev |
Release | Version | Architectures |
jessie | 1.3-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 1.4.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.4.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libssm-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
This package contains libraries and header files needed for program
development.
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Libssw-dev
Development headers and static libraries for libssw
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Versions of package libssw-dev |
Release | Version | Architectures |
sid | 1.1-2 | amd64,kfreebsd-amd64 |
buster | 1.1-2 | amd64 |
stretch | 1.1-1 | amd64 |
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License: DFSG free
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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.
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Libssw-java
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Versions of package libssw-java |
Release | Version | Architectures |
sid | 1.1-2 | amd64,kfreebsd-amd64 |
buster | 1.1-2 | amd64 |
stretch | 1.1-1 | amd64 |
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License: DFSG free
|
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.
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Libstaden-read-dev
development files for libstaden-read
|
Versions of package libstaden-read-dev |
Release | Version | Architectures |
wheezy | 1.12.4-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
squeeze | 1.12.4-1 | amd64,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mipsel,s390 |
jessie | 1.13.7-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 1.14.8-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.14.11-4 | kfreebsd-i386 |
buster | 1.14.11-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.14.11-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libstaden-read-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Libstatgen-dev
development files for the libStatGen
|
Versions of package libstatgen-dev |
Release | Version | Architectures |
sid | 1.0.14-4 | amd64,kfreebsd-amd64 |
buster | 1.0.14-4 | amd64 |
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License: DFSG free
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libStatGen is a library for statistical genetic programs. It includes some:
A. General Operation Classes including: File/Stream I/O, String processing
and Parameter Parsing.
B. Statistical Genetic Specific Classes including: Handling Common file
formats (Accessors to get/set values, Indexed access to BAM files) and
some utility classes, including: 1. Cigar: interpretation and mapping
between query and reference. 2. Pileup: structured access to data by
individual reference position.
This package provides the development files for libstatgen.
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Libswiss-perl
Perl API to the UniProt database
|
Versions of package libswiss-perl |
Release | Version | Architectures |
sid | 1.75-1 | all |
stretch | 1.67-1.1 | all |
squeeze | 1.67-1 | all |
wheezy | 1.67-1 | all |
jessie | 1.67-1 | all |
buster | 1.75-1 | all |
Debtags of package libswiss-perl: |
devel | lang:perl, library |
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License: DFSG free
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UniProt, SwissProt and TrEMBL are different views on protein sequence
data that is prepared by groups at the European Bioinformatics Institute
(EMBL-EBI) in Cambridge and the Swiss Bioinformatics Institute (SIB) at
the University Hospital in Geneva.
The SwissKnife Perl library is used by the developers of these databases
to perform all the automated editing and sytax checks. The users of
this package will profit from the stable API on an ever evolving
representation of biological knowledge.
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Libtabixpp-dev
C++ wrapper to tabix indexer (development files)
|
Versions of package libtabixpp-dev |
Release | Version | Architectures |
stretch | 1.0.0-2 | amd64,arm64,armel,i386,mips64el,mipsel,ppc64el |
buster | 1.0.0-4 | amd64,arm64,armel,armhf,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.0-4 | amd64,arm64,armel,armhf,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Libtfbs-perl
scanning DNA sequence with a position weight matrix
|
Versions of package libtfbs-perl |
Release | Version | Architectures |
buster | 0.7.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.7.1-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 0.5.svn.20091128-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
wheezy | 0.5.svn.20100421-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 0.6.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 0.7.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libtfbs-perl: |
field | biology, biology:bioinformatics |
role | devel-lib |
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License: DFSG free
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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".
Note: the TFBS perl module is no longer under active development. All the
functionality can be found in the TFBSTools Bioconductor package; users are
highly encouraged to switch. http://bioconductor.org/packages/TFBSTools/
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Libthread-pool-dev
C++ thread pool library (devel)
|
Versions of package libthread-pool-dev |
Release | Version | Architectures |
sid | 1.0.0-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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A thread pool is a software design pattern for achieving concurrency of
execution in a computer program. Often also called a replicated workers
or worker-crew model,[1] a thread pool maintains multiple threads
waiting for tasks to be allocated for concurrent execution by the
supervising program.
This package contains the static library and the header files.
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Libvcflib-dev
C++ library for parsing and manipulating VCF files (development)
|
Versions of package libvcflib-dev |
Release | Version | Architectures |
stretch | 1.0.0~rc1+dfsg1-3 | amd64 |
buster | 1.0.0~rc2+dfsg-2 | amd64 |
sid | 1.0.0~rc2+dfsg-2 | amd64,kfreebsd-amd64 |
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License: DFSG free
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The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
intended to concisely describe reference-indexed variations between
individuals. VCF provides a common interchange format for the description of
variation in individuals and populations of samples, and has become the defacto
standard reporting format for a wide array of genomic variant detectors.
vcflib provides methods to manipulate and interpret sequence variation as it
can be described by VCF. It is both:
- an API for parsing and operating on records of genomic variation as it can
be described by the VCF format,
- and a collection of command-line utilities for executing complex
manipulations on VCF files.
This package contains the static library and the header files.
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Libvibrant6-dev
NCBI libraries for graphic biology applications (development files)
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Versions of package libvibrant6-dev |
Release | Version | Architectures |
sid | 6.1.20170106-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 6.1.20090809-2 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
wheezy | 6.1.20120620-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
stretch | 6.1.20170106-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 6.1.20170106-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 6.1.20120620-8 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package libvibrant6-dev: |
biology | nuceleic-acids, peptidic |
devel | lang:c, library |
field | biology, biology:bioinformatics, biology:structural |
interface | 3d, x11 |
role | devel-lib |
science | visualisation |
uitoolkit | motif |
use | analysing, calculating, editing, viewing |
works-with | 3dmodel, biological-sequence |
works-with-format | plaintext, xml |
x11 | library |
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License: DFSG free
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Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
biological applications.
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Libzerg-perl
fast perl module for parsing the output of NCBI BLAST programs
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Versions of package libzerg-perl |
Release | Version | Architectures |
jessie | 1.0.4-3 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.0.4-7 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.4-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 1.0.4-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
stretch | 1.0.4-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libzerg-perl: |
devel | lang:perl, library |
role | shared-lib |
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License: DFSG free
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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.
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Libzerg0-dev
development libraries and header files for libzerg
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Versions of package libzerg0-dev |
Release | Version | Architectures |
wheezy | 1.0.7-3 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 1.0.7-10 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.7-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.0.7-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0.7-6 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
Debtags of package libzerg0-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
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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.
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Mcl
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Versions of package mcl |
Release | Version | Architectures |
sid | 14-137+ds-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 14-137+ds-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 14-137-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 12-068-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
jessie | 14-137-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
squeeze | 10-148-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
Debtags of package mcl: |
field | mathematics |
role | program |
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License: DFSG free
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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
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Pyfai
Fast Azimuthal Integration scripts
|
Versions of package pyfai |
Release | Version | Architectures |
sid | 0.14.2+dfsg-6 | all |
jessie | 0.10.2-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 0.17.0+dfsg1-3 | all |
wheezy | 0.3.5-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
buster | 0.17.0+dfsg1-3 | all |
stretch | 0.13.0+dfsg-1 | all |
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License: DFSG free
|
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.
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Python-biom-format
Biological Observation Matrix (BIOM) format (Python 2)
|
Versions of package python-biom-format |
Release | Version | Architectures |
sid | 2.1.6+dfsg-2 | kfreebsd-amd64,kfreebsd-i386 |
sid | 2.1.7+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
buster | 2.1.7+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 2.1.5+dfsg-7 | hurd-i386 |
stretch | 2.1.5+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
jessie | 2.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
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License: DFSG free
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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)
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Python-cogent
framework for genomic biology
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Versions of package python-cogent |
Release | Version | Architectures |
squeeze | 1.4.1-1.2 (non-free) | amd64,armel,i386,ia64,mips,mipsel,powerpc,s390,sparc |
sid | 1.9-14 | amd64,arm64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.5.3-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.5.3-2 | hurd-i386 |
stretch | 1.9-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.9-14 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 1.5.1-2 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
Debtags of package python-cogent: |
biology | peptidic |
devel | lang:python |
field | biology |
role | devel-lib |
use | analysing, comparing |
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License: DFSG free
|
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)
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Python-corepywrap
library that exports C++ mmCIF accessors to Python
|
Versions of package python-corepywrap |
Release | Version | Architectures |
stretch | 1.005-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.005-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.005-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.005-3 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
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License: DFSG free
|
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.
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Python-freecontact
fast protein contact predictor - binding for Python
|
Versions of package python-freecontact |
Release | Version | Architectures |
jessie | 1.1-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.1-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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?)
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Python-htseq
Python high-throughput genome sequencing read analysis utilities
|
Versions of package python-htseq |
Release | Version | Architectures |
stretch | 0.6.1p1-4 | amd64,arm64,mips64el,ppc64el |
sid | 0.5.4p3-2 | hurd-i386 |
sid | 0.6.1p1-4 | kfreebsd-amd64 |
jessie | 0.5.4p3-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 0.11.2-1 | amd64,arm64,mips64el,ppc64el |
buster | 0.11.2-1 | amd64,arm64,mips64el,ppc64el |
|
License: DFSG free
|
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.
This package contains the Python 2 module.
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Python-kineticstools
detection of DNA modifications (Python 2 library)
|
Versions of package python-kineticstools |
Release | Version | Architectures |
sid | 0.6.1+git20180425.27a1878-2 | amd64,arm64,kfreebsd-amd64,mips64el,ppc64el |
stretch | 0.6.1+20161222-1 | amd64,arm64,mips64el,ppc64el |
buster | 0.6.1+git20180425.27a1878-1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
|
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.
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Python-mmtk
molecular modeling toolkit
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Versions of package python-mmtk |
Release | Version | Architectures |
jessie | 2.7.9-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
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License: DFSG free
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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.
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Python-pbcommand
common command-line interface for Pacific Biosciences analysis modules
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Versions of package python-pbcommand |
Release | Version | Architectures |
sid | 1.1.1-1 | all |
buster | 1.1.1-1 | all |
stretch | 0.5.3-1 | all |
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License: DFSG free
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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.
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Python-pbcore
Python 2 library for processing PacBio data files
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Versions of package python-pbcore |
Release | Version | Architectures |
sid | 1.6.5+dfsg-1 | all |
buster | 1.6.5+dfsg-1 | all |
stretch | 1.2.11+dfsg-1 | all |
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License: DFSG free
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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.
This is the Python 2 module.
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Python-pbh5tools
tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
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Versions of package python-pbh5tools |
Release | Version | Architectures |
sid | 0.8.0+git20170929.58d54ff+dfsg-1 | amd64,arm64,kfreebsd-amd64,mips64el,ppc64el |
stretch | 0.8.0+dfsg-5 | amd64,arm64,mips64el,ppc64el |
buster | 0.8.0+git20170929.58d54ff+dfsg-1 | amd64,arm64,mips64el,ppc64el |
upstream | 0.8.0+git20181212.9fa8fc4 |
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License: DFSG free
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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
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Python-rdkit
Collection of cheminformatics and machine-learning software
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Versions of package python-rdkit |
Release | Version | Architectures |
sid | 201809.1+dfsg-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 201403-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 201603.5-2 | amd64,arm64,armel,i386,mips,mips64el,mipsel,ppc64el,s390x |
wheezy | 201203-3 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
buster | 201809.1+dfsg-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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 algorithm 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.
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Python-screed
short nucleotide read sequence utils in Python 2
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Versions of package python-screed |
Release | Version | Architectures |
stretch | 0.9-2 | all |
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License: DFSG free
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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.
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Python3-airr
Data Representation Standard library for antibody and TCR sequences
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Versions of package python3-airr |
Release | Version | Architectures |
buster | 1.2.1-2 | all |
sid | 1.2.1-2 | all |
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License: DFSG free
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This package provides a library by the AIRR community to for describing,
reporting, storing, and sharing adaptive immune receptor repertoire
(AIRR) data, such as sequences of antibodies and T cell receptors
(TCRs). Some specific efforts include:
- The MiAIRR standard for describing minimal information about AIRR
datasets, including sample collection and data processing information.
- Data representations (file format) specifications for storing large
amounts of annotated AIRR data.
- APIs for exposing a common interface to repositories/databases
containing AIRR data.
- A community standard for software tools which will allow conforming
tools to gain community recognition.
This package installs the library for Python 3.
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Python3-bcbio
library for analysing high-throughput sequencing data
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Versions of package python3-bcbio |
Release | Version | Architectures |
buster | 1.1.2-3 | all |
sid | 1.1.2-3 | all |
upstream | 1.1.3 |
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License: DFSG free
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This package installs the Python 3 libraries of the bcbio-nextgen
toolkit implementing best-practice pipelines for fully automated high
throughput sequencing analysis.
A high-level configuration file specifies inputs and analysis parameters
to drive a parallel pipeline that handles distributed execution,
idempotent processing restarts and safe transactional steps. The project
contributes a shared community resource that handles the data processing
component of sequencing analysis, providing researchers with more time
to focus on the downstream biology.
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Python3-biomaj3
BioMAJ workflow management library
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Versions of package python3-biomaj3 |
Release | Version | Architectures |
buster | 3.1.6-1 | all |
sid | 3.1.6-1 | all |
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License: DFSG free
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BioMAJ downloads remote data banks, checks their status and applies
transformation workflows, with consistent state, to provide ready-to-use
data for biologists and bioinformaticians. For example, it can transform
original FASTA files into BLAST indexes. It is very flexible and its
post-processing facilities can be extended very easily.
BioMAJ3 is a rewrite of BioMAJ v1.x, see online documentation for migration.
This package contains the library to manage the workflow update in BioMAJ3,
it is managed via python3-biomaj3-daemon (for microservices remote operations)
or biomaj3-cli (local or remote) packages
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Python3-biopython
Python library for bioinformatics (implemented in Python 3)
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Versions of package python3-biopython |
Release | Version | Architectures |
jessie | 1.64+dfsg-5 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 1.68+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.72+dfsg-1 | kfreebsd-amd64,kfreebsd-i386 |
buster | 1.73+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.73+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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)
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Python3-biotools
Python3 bioinformatics utilities for high-throughput genomic sequencing
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Versions of package python3-biotools |
Release | Version | Architectures |
sid | 1.2.12-3 | all |
buster | 1.2.12-3 | all |
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License: DFSG free
|
This package contains utilities like
biotools.align - align sequences (hybrid between Needleman-Wunsch and
Smith-Waterman which is used to find the subsequence
within a larger sequence that best aligns to a reference)
biotools.annotation - create annotation files. The annotations can be used
to create a hierarchy among the annotations
biotools.BLAST - manage BLAST databases and interface with the BLAST+
standalone program available from NCBI.
biotools.clustal - interface to clustalw global (multiple nucleotide or
peptide sequence alignment)
biotools.complement - creates the complement of a sequence, which can then be
reversed
biotools.sequence - various tools to deal with sequences
biotools.translate - translate a nucleotide using the standard genetic code
This package contains the Python3 module.
Please cite:
Rebecca Bart, Megan Cohn, Andrew Kassen, Emily J. McCallum, Mikel Shybut, Annalise Petriello, Ksenia Krasileva, Douglas Dahlbeck, Cesar Medina, Titus Alicai, Lava Kumar, Leandro M. Moreira, Júlio Rodrigues Neto, Valerie Verdier, María Angélica Santana, Nuttima Kositcharoenkul, Hervé Vanderschuren, Wilhelm Gruissem, Adriana Bernal and Brian J. Staskawicz:
High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance.
(PubMed)
PNAS
109(28):E1972-9
(2012)
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Python3-bx
library to manage genomic data and its alignment
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Versions of package python3-bx |
Release | Version | Architectures |
sid | 0.8.2-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.8.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
The bx-python project is a python library and associated set of scripts to
allow for rapid implementation of genome scale analyses. The library contains
a variety of useful modules, but the particular strengths are:
- Classes for reading and working with genome-scale multiple local
alignments (in MAF, AXT, and LAV formats)
- Generic data structure for indexing on disk files that contain blocks of
data associated with intervals on various sequences (used, for example, to
provide random access to individual alignments in huge files; optimized for
use over network filesystems)
- Data structures for working with intervals on sequences
- "Binned bitsets" which act just like chromosome sized bit arrays, but
lazily allocate regions and allow large blocks of all set or all unset bits
to be stored compactly
- "Intersecter" for performing fast intersection tests that preserve both
query and target intervals and associated annotation
This package provides the Python 3 library.
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Python3-cobra
constraint-based modeling of biological networks with Python 3
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Versions of package python3-cobra |
Release | Version | Architectures |
sid | 0.5.9-1 | kfreebsd-amd64,kfreebsd-i386 |
sid | 0.14.1-1 | hurd-i386,mips,mips64el,s390x |
sid | 0.14.2-1 | amd64,arm64,armel,armhf,i386,mipsel,ppc64el |
buster | 0.14.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.5.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
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Python3-csb
Python framework for structural bioinformatics (Python3 version)
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Versions of package python3-csb |
Release | Version | Architectures |
sid | 1.2.5+dfsg-3 | all |
jessie | 1.2.3+dfsg-1 | all |
stretch | 1.2.3+dfsg-3 | all |
buster | 1.2.5+dfsg-3 | all |
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License: DFSG free
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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.
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Python3-cutadapt
Clean biological sequences from high-throughput sequencing reads (Python 3)
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Versions of package python3-cutadapt |
Release | Version | Architectures |
buster | 1.18-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.18-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.12-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Python3-cyvcf2
VCF parser based on htslib (Python 3)
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Versions of package python3-cyvcf2 |
Release | Version | Architectures |
sid | 0.10.4-1 | mips64el |
buster | 0.10.4-1 | amd64,arm64,armel,armhf,i386,mips64el |
sid | 0.10.8-1 | amd64,arm64,armel,armhf,i386,mipsel |
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License: DFSG free
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This modules allows fast parsing of VCF and BCF including region-queries
with Python. This is essential for efficient analyses of nucleotide
variation with Python on high-throughput sequencing data.
cyvcf2 is a cython wrapper around htslib. Attributes like
variant.gt_ref_depths return a numpy array directly so they are
immediately ready for downstream use.
This package installs the library for Python 3.
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Python3-dendropy
DendroPy Phylogenetic Computing Library (Python 3)
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Versions of package python3-dendropy |
Release | Version | Architectures |
buster | 4.4.0-1 | all |
sid | 4.4.0-1 | all |
stretch | 4.2.0+dfsg-1 | all |
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License: DFSG free
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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.
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Python3-fast5
library for reading Oxford Nanopore Fast5 files -- Python 3
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Versions of package python3-fast5 |
Release | Version | Architectures |
sid | 0.6.5-2 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.5.8-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.6.5-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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A lightweight C++11 library to read raw signal data from Oxford
Nanopore's FAST5 files.
This package provides the Python 3 library
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Python3-gfapy
flexible and extensible software library for handling sequence graphs
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Versions of package python3-gfapy |
Release | Version | Architectures |
buster | 1.0.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.0+dfsg-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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The Graphical Fragment Assembly (GFA) are formats for the representation of
sequence graphs, including assembly, variation and splicing graphs. Two
versions of GFA have been defined (GFA1 and GFA2) and several sequence
analysis programs have been adopting the formats as an interchange format,
which allow the user to easily combine different sequence analysis tools.
This library implements the GFA1 and GFA2 specification. It is possible to
create a Gfa object from a file in the GFA format or from scratch, to
enumerate the graph elements (segments, links, containments, paths and header
lines), to traverse the graph (by traversing all links outgoing from or
incoming to a segment), to search for elements (e.g. which links connect two
segments) and to manipulate the graph (e.g. to eliminate a link or a segment
or to duplicate a segment distributing the read counts evenly on the copies).
The GFA format can be easily extended by users by defining own custom tags
and record types. In Gfapy, it is easy to write extensions modules, which
allow one to define custom record types and datatypes for the parsing and
validation of custom fields. The custom lines can be connected, using
references, to each other and to lines of the standard record types.
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Python3-gffutils
Work with GFF and GTF files in a flexible database framework
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Versions of package python3-gffutils |
Release | Version | Architectures |
buster | 0.9-1 | all |
sid | 0.9-1 | all |
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License: DFSG free
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A Python package for working with and manipulating the GFF and GTF format
files typically used for genomic annotations. Files are loaded into a
sqlite3 database, allowing much more complex manipulation of hierarchical
features (e.g., genes, transcripts, and exons) than is possible with
plain-text methods alone.
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Python3-intervaltree-bio
Interval tree convenience classes for genomic data -- Python 3 library
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Versions of package python3-intervaltree-bio |
Release | Version | Architectures |
buster | 1.0.1-3 | all |
sid | 1.0.1-3 | all |
stretch | 1.0.1-1 | all |
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License: DFSG free
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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.
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Python3-ngs
Next Generation Sequencing language Bindings (Python3 bindings)
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Versions of package python3-ngs |
Release | Version | Architectures |
sid | 2.9.3-1 | amd64,i386 |
buster | 2.9.3-1 | amd64,i386 |
stretch | 1.3.0-2 | amd64,i386 |
upstream | 2.9.4 |
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License: DFSG free
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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.
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Python3-pbconsensuscore
algorithms for PacBio multiple sequence consensus -- Python 3
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Versions of package python3-pbconsensuscore |
Release | Version | Architectures |
sid | 1.1.1+dfsg-1 | amd64,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386 |
buster | 1.1.1+dfsg-1 | amd64,i386 |
stretch | 1.0.2-2 | amd64,i386 |
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License: DFSG free
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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.
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Python3-presto
toolkit for processing B and T cell sequences
|
Versions of package python3-presto |
Release | Version | Architectures |
buster | 0.5.10-1 | all |
sid | 0.5.10-1 | all |
upstream | 0.5.11 |
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License: DFSG free
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pRESTO is a toolkit for processing raw reads from high-throughput
sequencing of B cell and T cell repertoires.
Dramatic improvements in high-throughput sequencing technologies now
enable large-scale characterization of lymphocyte repertoires, defined
as the collection of trans-membrane antigen-receptor proteins located on
the surface of B cells and T cells. The REpertoire Sequencing TOolkit
(pRESTO) is composed of a suite of utilities to handle all stages
of sequence processing prior to germline segment assignment. pRESTO
is designed to handle either single reads or paired-end reads. It
includes features for quality control, primer masking, annotation of
reads with sequence embedded barcodes, generation of unique molecular
identifier (UMI) consensus sequences, assembly of paired-end reads and
identification of duplicate sequences. Numerous options for sequence
sorting, sampling and conversion operations are also included.
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Python3-pybedtools
Python 3 wrapper around BEDTools for bioinformatics work
|
Versions of package python3-pybedtools |
Release | Version | Architectures |
sid | 0.8.0-1 | amd64,arm64,mips64el,ppc64el |
buster | 0.8.0-1 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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The BEDTools suite of programs is widely used for genomic interval
manipulation or “genome algebra”. pybedtools wraps and extends BEDTools and
offers feature-level manipulations from within Python.
This is the Python 3 version.
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Python3-pybel
Biological Expression Language
|
Versions of package python3-pybel |
Release | Version | Architectures |
buster | 0.12.1-1 | all |
experimental | 0.13.1-1 | all |
sid | 0.12.1-1 | all |
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License: DFSG free
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PyBEL is a pure Python package for parsing and handling biological
networks encoded in the Biological Expression Language (BEL) version
2. It also facilitates data interchange between common formats and
databases such as NetworkX, JSON, CSV, SIF, Cytoscape, CX, NDEx, SQL,
and Neo4J.
This package installs the library for Python 3.
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Python3-pyfaidx
efficient random access to fasta subsequences for Python 3
|
Versions of package python3-pyfaidx |
Release | Version | Architectures |
stretch | 0.4.8.1-1 | all |
buster | 0.5.5.2-1 | all |
sid | 0.5.5.2-1 | all |
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License: DFSG free
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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.
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Python3-pymummer
Python 3 interface to MUMmer
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Versions of package python3-pymummer |
Release | Version | Architectures |
buster | 0.10.3-2 | all |
stretch | 0.10.1-1 | all |
sid | 0.10.3-2 | all |
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License: DFSG free
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pymummer is a Python wrapper for running the programs of the MUMmer
sequence alignment suite and parsing their output.
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Python3-pysam
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
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Versions of package python3-pysam |
Release | Version | Architectures |
stretch | 0.10.0+ds-2 | amd64,arm64,mips64el,ppc64el |
buster | 0.15.1+ds-1 | amd64,arm64,mips64el,ppc64el |
sid | 0.15.1+ds-1 | kfreebsd-amd64 |
sid | 0.15.2+ds-2 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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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 3.
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Python3-pyvcf
Variant Call Format (VCF) parser for Python 3
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Versions of package python3-pyvcf |
Release | Version | Architectures |
sid | 0.6.8+git20170215.476169c-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.6.8+git20170215.476169c-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.6.8-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Python3-ruffus
Python3 computation pipeline library widely used in bioinformatics
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Versions of package python3-ruffus |
Release | Version | Architectures |
sid | 2.8.1-4 | all |
stretch | 2.6.3+dfsg-4 | all |
buster | 2.8.1-4 | all |
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License: DFSG free
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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.
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Python3-screed
short nucleotide read sequence utils in Python 3
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Versions of package python3-screed |
Release | Version | Architectures |
stretch | 0.9-2 | all |
sid | 1.0-3 | all |
buster | 1.0-3 | all |
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License: DFSG free
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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.
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Python3-skbio
Python3 data structures, algorithms, educational resources for bioinformatic
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Versions of package python3-skbio |
Release | Version | Architectures |
stretch | 0.5.1-2 | amd64 |
sid | 0.5.2-1 | kfreebsd-amd64 |
sid | 0.5.5-2 | amd64 |
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License: DFSG free
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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
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Python3-sqt
SeQuencing Tools for biological DNA/RNA high-throughput data
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Versions of package python3-sqt |
Release | Version | Architectures |
sid | 0.8.0-3 | amd64,arm64,mips64el,ppc64el |
buster | 0.8.0-3 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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sqt is a collection of command-line tools for working with
high-throughput sequencing data. Conceptionally not fixed to use any
particular language, many sqt subcommands are currently implemented
in Python. For them, a Python package is available with functions for
reading and writing FASTA/FASTQ files, computing alignments, quality
trimming, etc.
The following tools are offered:
- sqt-coverage -- Compute per-reference statistics such as coverage
and GC content
- sqt-fastqmod -- FASTQ modifications: shorten, subset, reverse
complement, quality trimming.
- sqt-fastastats -- Compute N50, min/max length, GC content etc. of
a FASTA file
- sqt-qualityguess -- Guess quality encoding of one or more FASTA files.
- sqt-globalalign -- Compute a global or semiglobal alignment of two strings.
- sqt-chars -- Count length of the first word given on the command line.
- sqt-sam-cscq -- Add the CS and CQ tags to a SAM file with colorspace reads.
- sqt-fastamutate -- Add substitutions and indels to sequences in a
FASTA file.
- sqt-fastaextract -- Efficiently extract one or more regions from an
indexed FASTA file.
- sqt-translate -- Replace characters in FASTA files (like the 'tr'
command).
- sqt-sam-fixn -- Replace all non-ACGT characters within reads in a
SAM file.
- sqt-sam-insertsize -- Mean and standard deviation of paired-end
insert sizes.
- sqt-sam-set-op -- Set operations (union, intersection, ...) on
SAM/BAM files.
- sqt-bam-eof -- Check for the End-Of-File marker in compressed
BAM files.
- sqt-checkfastqpe -- Check whether two FASTQ files contain correctly
paired paired-end data.
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Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
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Versions of package python3-treetime |
Release | Version | Architectures |
buster | 0.5.3-1 | all |
sid | 0.5.3-1 | all |
upstream | 0.5.4 |
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License: DFSG free
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TreeTime provides routines for ancestral sequence reconstruction and the
maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
where all branches are scaled such that the locations of terminal nodes
correspond to their sampling times and internal nodes are placed at the
most likely time of divergence.
TreeTime aims at striking a compromise between sophisticated
probabilistic models of evolution and fast heuristics. It implements GTR
models of ancestral inference and branch length optimization, but takes
the tree topology as given. To optimize the likelihood of time-scaled
phylogenies, treetime uses an iterative approach that first infers
ancestral sequences given the branch length of the tree, then optimizes
the positions of unconstraine d nodes on the time axis, and then repeats
this cycle. The only topology optimization are (optional) resolution of
polytomies in a way that is most (approximately) consistent with the
sampling time constraints on the tree. The package is designed to be
used as a stand-alone tool or as a library used in larger phylogenetic
analysis workflows.
Features
- ancestral sequence reconstruction (marginal and joint maximum
likelihood)
- molecular clock tree inference (marginal and joint maximum
likelihood)
- inference of GTR models
- rerooting to obtain best root-to-tip regression
- auto-correlated relaxed molecular clock (with normal prior)
This package provides the Python 3 module.
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R-bioc-biobase
base functions for Bioconductor
|
Versions of package r-bioc-biobase |
Release | Version | Architectures |
wheezy | 2.14.0-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
buster | 2.42.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.24.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 2.42.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 2.34.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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)
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R-cran-genetics
GNU R package for population genetics
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Versions of package r-cran-genetics |
Release | Version | Architectures |
squeeze | 1.3.4-1 | all |
sid | 1.3.8.1.1-1 | all |
buster | 1.3.8.1.1-1 | all |
stretch | 1.3.8.1-1 | all |
jessie | 1.3.8.1-1 | all |
wheezy | 1.3.6-2 | all |
Debtags of package r-cran-genetics: |
devel | lang:r |
field | biology, biology:bioinformatics, biology:molecular, biology:structural |
use | analysing |
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License: DFSG free
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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.
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R-cran-haplo.stats
GNU R package for haplotype analysis
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Versions of package r-cran-haplo.stats |
Release | Version | Architectures |
wheezy | 1.5.5-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
sid | 1.7.9-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.7.9-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.7.7-1 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.6.11-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
squeeze | 1.4.4-1 | amd64,armel,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,sparc |
Debtags of package r-cran-haplo.stats: |
devel | lang:r |
field | biology, biology:bioinformatics |
use | analysing |
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License: DFSG free
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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.
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R-cran-phylobase
GNU R base package for phylogenetic structures and comparative data
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Versions of package r-cran-phylobase |
Release | Version | Architectures |
sid | 0.8.6-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.8.6-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.8.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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R-cran-rncl
GNU R interface to the Nexus Class Library
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Versions of package r-cran-rncl |
Release | Version | Architectures |
buster | 0.8.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 0.8.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.8.3-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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)'.
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R-cran-rnexml
GNU R package for semantically rich I/O for the 'NeXML' format
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Versions of package r-cran-rnexml |
Release | Version | Architectures |
stretch | 2.0.7-1 | all |
sid | 2.3.0-1 | all |
buster | 2.3.0-1 | all |
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License: DFSG free
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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.
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Ruby-bio
Ruby tools for computational molecular biology
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Versions of package ruby-bio |
Release | Version | Architectures |
stretch | 1.5.0-2 | all |
sid | 1.5.2-1 | all |
jessie | 1.4.3.0001-2 | all |
wheezy | 1.4.2-3 | all |
buster | 1.5.2-1 | all |
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License: DFSG free
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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.
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Ruby-crb-blast
Run conditional reciprocal best blast
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Versions of package ruby-crb-blast |
Release | Version | Architectures |
stretch | 0.6.8-1 | all |
sid | 0.6.9-2 | all |
buster | 0.6.9-2 | all |
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License: DFSG free
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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.
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Sbmltoolbox
libsbml toolbox for octave and matlab
|
Versions of package sbmltoolbox |
Release | Version | Architectures |
jessie | 4.1.0-1 | all |
buster | 4.1.0-4 | all |
sid | 4.1.0-4 | all |
stretch | 4.1.0-3 | all |
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License: DFSG free
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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.
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Seqan-dev
C++ library for the analysis of biological sequences (development)
|
Versions of package seqan-dev |
Release | Version | Architectures |
sid | 1.4.2+dfsg-3 | all |
jessie | 1.4.1+dfsg-2 | all |
squeeze | 1.2-1 | all |
stretch | 1.4.2+dfsg-2 | all |
buster | 1.4.2+dfsg-3 | all |
wheezy | 1.3.1-1 | all |
Debtags of package seqan-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
|
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.
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Snakemake
pythonic workflow management system
|
Versions of package snakemake |
Release | Version | Architectures |
stretch | 3.10.0-1 | all |
sid | 5.4.0-1 | all |
buster | 5.4.0-1 | all |
upstream | 5.4.2 |
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License: DFSG free
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Build systems like GNU Make are frequently used to create complicated
workflows, e.g. in bioinformatics. This project aims to reduce the
complexity of creating workflows by providing a clean and modern domain
specific language (DSL) in Python style, together with a fast and
comfortable execution environment.
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Toil
cross-platform workflow engine
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Versions of package toil |
Release | Version | Architectures |
sid | 3.18.0-2 | all |
buster | 3.18.0-2 | all |
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License: DFSG free
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Toil is a scalable, efficient, cross-platform and easy-to-use workflow
engine in pure Python. It works with several well established load
balancers like Slurm or the Sun Grid Engine. Toil is also compatible with
the Common Workflow Language (CWL) via the "toil-cwl-runner" interface, which
this package make available via the Debian alternativess system under the
alias "cwl-runner".
Please cite:
John Vivian, Arjun Arkal Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, Melissa Cline, Brian O'Connor, Megan Hanna, Chet Birger, W. James Kent David A. Patterson, Anthony D. Joseph, Jingchun Zhu, Sasha Zaranek, Gad Getz, David Haussler and Benedict Paten:
Toil enables reproducible, open source, big biomedical data analyses.
Nature Biotechnology
35(4):314–316
(2017)
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Official Debian packages with lower relevance
Ctdconverter
Convert CTD files into Galaxy tool and CWL CommandLineTool files
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Versions of package ctdconverter |
Release | Version | Architectures |
sid | 2.0-4 | all |
buster | 2.0-4 | all |
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License: DFSG free
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Common Tool Descriptors (CTDs) are XML documents that represent the inputs,
outputs, parameters of command line tools in a platform-independent way.
CTDConverter, given one or more Common Tool Descriptors (CTD) XML files,
generates Galaxy tool wrappers and Common Workflow Language (CWL) Command
Line Tool v1.0 standard descriptions from CTD files.
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Libbam-dev
manipulates nucleotide sequence alignments in BAM or SAM format
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Versions of package libbam-dev |
Release | Version | Architectures |
stretch | 0.1.19-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
squeeze | 0.1.8-1 | amd64,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390 |
wheezy | 0.1.18-1 | amd64,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390 |
jessie | 0.1.19-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 0.1.19-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.1.19-4 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libbam-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
|
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.
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Libdisorder-dev
library for entropy measurement of byte streams (devel)
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Versions of package libdisorder-dev |
Release | Version | Architectures |
stretch | 0.0.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el |
buster | 0.0.2+git20130809.8062ee1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.0.2+git20130809.8062ee1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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Libfreecontact-doc
documentation for libfreecontact
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Versions of package libfreecontact-doc |
Release | Version | Architectures |
buster | 1.0.21-7 | all |
stretch | 1.0.21-5 | all |
jessie | 1.0.21-3 | all |
sid | 1.0.21-7 | all |
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License: DFSG free
|
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.
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Libgtextutils-dev
Gordon Text_utils library (development files)
|
Versions of package libgtextutils-dev |
Release | Version | Architectures |
jessie | 0.7-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
wheezy | 0.6.2-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
stretch | 0.7-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.7-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.7-6 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package libgtextutils-dev: |
devel | library |
role | devel-lib |
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License: DFSG free
|
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.
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Libmilib-java
library for Next Generation Sequencing (NGS) data processing
|
Versions of package libmilib-java |
Release | Version | Architectures |
buster | 1.8.4-1 | all |
sid | 1.10-2 | all |
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License: DFSG free
|
A helping Java package adopted by a range of Open Source tools for the
analysis of B and T cell repertoires.
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Libmodhmm-dev
library for constructing, training and scoring hidden Markov models (dev)
|
Versions of package libmodhmm-dev |
Release | Version | Architectures |
buster | 1.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0+dfsg-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Library for constructing, training and scoring hidden Markov models. It
is provided with PSORTb but might be used separately.
PSORTb enables prediction of bacterial protein subcellular localization
(SCL) and provides a quick and inexpensive means for gaining insight
into protein function, verifying experimental results, annotating newly
sequenced bacterial genomes, detecting potential cell surface/secreted
drug targets, as well as identifying biomarkers for microbes.
This library needed by PSORTb is distributed separately by upstream.
This package contains the static library which is needed to link PSORTb.
Please cite:
Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster and F. S. Brinkman:
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
(PubMed,eprint)
Bioinformatics
26(13):1608-1615
(2010)
|
|
Libpbcopper-dev
data structures, algorithms, and utilities for C++ applications -- header files
|
Versions of package libpbcopper-dev |
Release | Version | Architectures |
buster | 0.4.1+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.4.1+dfsg-2 | amd64,arm64,armel,armhf,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
pbcopper provides general tools for C++ applications. It is developed
for use by applications of the Pacific Biosciences SMRT Analysis
suite.
This package contains the header files and static library
|
|
Librostlab-blast-doc
very fast C++ library for parsing the output of NCBI BLAST programs (doc)
|
Versions of package librostlab-blast-doc |
Release | Version | Architectures |
buster | 1.0.1-9 | all |
wheezy | 1.0.0-2 | all |
jessie | 1.0.1-3 | all |
sid | 1.0.1-9 | all |
stretch | 1.0.1-7 | all |
|
License: DFSG free
|
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)
|
Versions of package librostlab-doc |
Release | Version | Architectures |
stretch | 1.0.20-6 | all |
jessie | 1.0.20-4 | all |
wheezy | 1.0.20-1 | all |
sid | 1.0.20-8 | all |
buster | 1.0.20-8 | all |
|
License: DFSG free
|
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.
|
|
Libsvmloc-dev
PSORTb adapted library for svm machine-learning library (dev)
|
Versions of package libsvmloc-dev |
Release | Version | Architectures |
buster | 1.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.0+dfsg-3 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
Libsvm is a machine-learning library which is an easy-to-use package
for support vector classification, regression and one-class SVM. It
supports multi-class classification, probability outputs, and
parameter selection.
PSORTb was featuring a code copy plus some local additions. This
library is linked against the Debian packaged libsvn and just contains
the PSORTb extensions.
PSORTb enables prediction of bacterial protein subcellular localization
(SCL) and provides a quick and inexpensive means for gaining insight
into protein function, verifying experimental results, annotating newly
sequenced bacterial genomes, detecting potential cell surface/secreted
drug targets, as well as identifying biomarkers for microbes.
This library needed by PSORTb is distributed separately by upstream.
This package contains the static library which is needed to link PSORTb.
Please cite:
Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster and F. S. Brinkman:
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.
(PubMed,eprint)
Bioinformatics
26(13):1608-1615
(2010)
|
|
Python-biopython-doc
Documentation for the Biopython library
|
Versions of package python-biopython-doc |
Release | Version | Architectures |
buster | 1.73+dfsg-1 | all |
sid | 1.72+dfsg-1 | all |
stretch | 1.68+dfsg-3 | all |
jessie | 1.64+dfsg-5 | all |
wheezy | 1.59-1 | all |
squeeze | 1.54-1 | all |
sid | 1.73+dfsg-1 | all |
Debtags of package python-biopython-doc: |
devel | doc, lang:python |
field | biology, biology:bioinformatics |
role | documentation |
|
License: DFSG free
|
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-pyflow
lightweight parallel task engine for Python
|
Versions of package python-pyflow |
Release | Version | Architectures |
buster | 1.1.20-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.1.20-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
pyFlow is a tool to manage tasks in the context of a task dependency
graph. It has some similarities to make. pyFlow is not a program – it is
a Python module, and workflows are defined using pyFlow by writing
regular Python code with the pyFlow API.
|
|
Python3-biopython-sql
Biopython support for the BioSQL database schema (Python 3)
|
Versions of package python3-biopython-sql |
Release | Version | Architectures |
jessie | 1.64+dfsg-5 | all |
sid | 1.72+dfsg-1 | all |
sid | 1.73+dfsg-1 | all |
stretch | 1.68+dfsg-3 | all |
buster | 1.73+dfsg-1 | all |
|
License: DFSG free
|
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)
|
|
Python3-ctdopts
Gives your Python tools a CTD-compatible interface
|
Versions of package python3-ctdopts |
Release | Version | Architectures |
buster | 1.2-3 | all |
sid | 1.2-3 | all |
|
License: DFSG free
|
Common Tool Descriptors (CTDs) are XML documents that represent the inputs,
outputs, parameters of command line tools in a platform-independent way.
CTDopts is a module for enabling tools with CTD reading/writing, argument
parsing, validating and manipulating capabilities.
|
|
R-bioc-affy
BioConductor methods for Affymetrix Oligonucleotide Arrays
|
Versions of package r-bioc-affy |
Release | Version | Architectures |
sid | 1.60.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.52.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.60.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.42.3-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
|
License: DFSG free
|
This is part of the BioConductor GNU R suite. The package contains
functions for exploratory oligonucleotide array analysis.
|
|
R-bioc-affyio
BioConductor tools for parsing Affymetrix data files
|
Versions of package r-bioc-affyio |
Release | Version | Architectures |
jessie | 1.32.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 1.52.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.44.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.52.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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
|
Versions of package r-bioc-altcdfenvs |
Release | Version | Architectures |
sid | 2.44.0-1 | all |
jessie | 2.26.0-1 | all |
stretch | 2.36.0-1 | all |
buster | 2.44.0-1 | all |
|
License: DFSG free
|
This BioConductor module provides alternative CDF environments (aka
probeset mappings) which are Convenience data structures and functions
to handle cdfenvs.
|
|
R-bioc-annotationdbi
GNU R Annotation Database Interface for BioConductor
|
Versions of package r-bioc-annotationdbi |
Release | Version | Architectures |
stretch | 1.36.1-2 | all |
sid | 1.44.0-1 | all |
buster | 1.44.0-1 | all |
jessie | 1.26.1-1 | all |
|
License: DFSG free
|
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
|
Versions of package r-bioc-biocgenerics |
Release | Version | Architectures |
jessie | 0.10.0-1 | all |
stretch | 0.20.0-1 | all |
buster | 0.28.0-2 | all |
sid | 0.28.0-2 | all |
wheezy | 0.2.0-1 | amd64,armel,armhf,i386,ia64,kfreebsd-amd64,kfreebsd-i386,mips,mipsel,powerpc,s390,s390x,sparc |
|
License: DFSG free
|
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.
Please cite:
Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D Hansen, Rafael A Irizarry, Michael Lawrence, Michael I Love, James MacDonald, Valerie Obenchain, Andrzej K Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K Smyth, Dan Tenenbaum, Levi Waldron and Martin Morgan:
Orchestrating high-throughput genomic analysis with Bioconductor.
(PubMed)
Nature Methods
(2015)
|
|
R-bioc-biomart
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
|
Versions of package r-bioc-biomart |
Release | Version | Architectures |
sid | 2.38.0+dfsg-1 | all |
stretch | 2.30.0-1 | all |
jessie | 2.20.0-1 | all |
buster | 2.38.0+dfsg-1 | all |
|
License: DFSG free
|
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.
|
|
R-bioc-biomformat
GNU R interface package for the BIOM file format
|
Versions of package r-bioc-biomformat |
Release | Version | Architectures |
sid | 1.10.1+dfsg-1 | all |
buster | 1.10.1+dfsg-1 | all |
stretch | 1.2.0-1 | all |
|
License: DFSG free
|
This is an R package for interfacing with the BIOM format. This package
includes basic tools for reading biom-format files, accessing and
subsetting data tables from a biom object (which is more complex than a
single table), as well as limited support for writing a biom-object back
to a biom-format file. The design of this API is intended to match the
Python API and other tools included with the biom-format project, but
with a decidedly "R flavor" that should be familiar to R users. This
includes S4 classes and methods, as well as extensions of common core
functions/methods.
|
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R-bioc-biovizbase
GNU R basic graphic utilities for visualization of genomic data
|
Versions of package r-bioc-biovizbase |
Release | Version | Architectures |
stretch | 1.22.0-2 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.30.1-1 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.12.3-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.30.1-1 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
|
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R-bioc-bsgenome
BioConductor infrastructure for Biostrings-based genome data packages
|
Versions of package r-bioc-bsgenome |
Release | Version | Architectures |
stretch | 1.42.0-2 | all |
jessie | 1.32.0-1 | all |
sid | 1.50.0-1 | all |
buster | 1.50.0-1 | all |
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License: DFSG free
|
This BioConductor module provides some basic infrastructure for
Biostrings-based genome data packages.
|
|
R-bioc-genomeinfodb
BioConductor utilities for manipulating chromosome identifiers
|
Versions of package r-bioc-genomeinfodb |
Release | Version | Architectures |
buster | 1.18.1-1 | all |
jessie | 1.0.2-2 | all |
sid | 1.18.1-1 | all |
stretch | 1.10.3-1 | all |
upstream | 1.18.2 |
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License: DFSG free
|
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.
|
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R-bioc-genomicalignments
BioConductor representation and manipulation of short genomic alignments
|
Versions of package r-bioc-genomicalignments |
Release | Version | Architectures |
jessie | 1.0.6-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.18.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.10.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.18.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
|
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R-bioc-genomicfeatures
GNU R tools for making and manipulating transcript centric annotations
|
Versions of package r-bioc-genomicfeatures |
Release | Version | Architectures |
jessie | 1.16.3-1 | all |
stretch | 1.26.2-1 | all |
buster | 1.34.3+dfsg-1 | all |
sid | 1.34.3+dfsg-1 | all |
|
License: DFSG free
|
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.
|
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R-bioc-genomicranges
BioConductor representation and manipulation of genomic intervals
|
Versions of package r-bioc-genomicranges |
Release | Version | Architectures |
jessie | 1.16.4-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.34.0+dfsg-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.34.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.26.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
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.
|
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R-bioc-graph
handle graph data structures for BioConductor
|
Versions of package r-bioc-graph |
Release | Version | Architectures |
sid | 1.60.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.52.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.42.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 1.60.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
|
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R-bioc-hypergraph
BioConductor hypergraph data structures
|
Versions of package r-bioc-hypergraph |
Release | Version | Architectures |
sid | 1.54.0-1 | all |
jessie | 1.36.0-1 | all |
stretch | 1.46.0-1 | all |
buster | 1.54.0-1 | all |
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License: DFSG free
|
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
|
Versions of package r-bioc-iranges |
Release | Version | Architectures |
sid | 2.16.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.22.10-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 2.8.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.16.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
|
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R-bioc-makecdfenv
BioConductor CDF Environment Maker
|
Versions of package r-bioc-makecdfenv |
Release | Version | Architectures |
buster | 1.58.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.40.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 1.50.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.58.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
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.
|
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R-bioc-preprocesscore
BioConductor collection of pre-processing functions
|
Versions of package r-bioc-preprocesscore |
Release | Version | Architectures |
stretch | 1.36.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.44.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.44.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.26.1-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
|
License: DFSG free
|
This BioConductor module contains a library of pre-processing
functions. It is imported by several other BioConductor modules.
|
|
R-bioc-rbgl
R interface to the graph algorithms contained in the BOOST library
|
Versions of package r-bioc-rbgl |
Release | Version | Architectures |
buster | 1.58.1+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.50.0+dfsg1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.58.1+dfsg-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
RBGL is part of the BioConductor GNU R suite. It is a fairly extensive and
comprehensive interface to the graph algorithms contained in the BOOST C++
libraries.
|
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R-bioc-rsamtools
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
|
Versions of package r-bioc-rsamtools |
Release | Version | Architectures |
stretch | 1.26.1-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.34.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.16.1-2 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
sid | 1.34.1-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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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.
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R-bioc-shortread
GNU R classes and methods for high-throughput short-read sequencing data
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Versions of package r-bioc-shortread |
Release | Version | Architectures |
stretch | 1.32.0-1 | amd64,arm64,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.40.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.40.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.22.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
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License: DFSG free
|
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.
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R-bioc-snpstats
BioConductor SnpMatrix and XSnpMatrix classes and methods
|
Versions of package r-bioc-snpstats |
Release | Version | Architectures |
sid | 1.32.0+dfsg-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.14.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
buster | 1.32.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
stretch | 1.24.0+dfsg-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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This BioConductor package provides R functions to work with
SnpMatrix and XSnpMatrix classes and methods.
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R-bioc-variantannotation
BioConductor annotation of genetic variants
|
Versions of package r-bioc-variantannotation |
Release | Version | Architectures |
sid | 1.28.10-1 | amd64,arm64,armel,armhf,hurd-i386,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.28.10-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.10.5-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
stretch | 1.20.2-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
upstream | 1.28.11 |
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License: DFSG free
|
This BioConductor package provides R functions to annotate variants,
compute amino acid coding changess and to predict coding outcomes.
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R-bioc-xvector
BioConductor representation and manpulation of external sequences
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Versions of package r-bioc-xvector |
Release | Version | Architectures |
stretch | 0.14.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 0.22.0-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.22.0-1 | amd64,arm64,armel,armhf,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.4.0-1 | amd64,arm64,armel,armhf,i386,mips,mipsel,powerpc,ppc64el,s390x |
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License: DFSG free
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This BioConductor package provides memory efficient S4 classes for storing
sequences "externally" (behind an R external pointer, or on disk).
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R-cran-natserv
GNU R 'NatureServe' Interface
|
Versions of package r-cran-natserv |
Release | Version | Architectures |
buster | 0.3.0+dfsg-2 | all |
sid | 0.3.0+dfsg-2 | all |
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License: DFSG free
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Interface to 'NatureServe' (http://www.natureserve.org).
Includes methods to get data, image metadata, search taxonomic names,
and make maps.
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R-cran-rentrez
GNU R interface to the NCBI's EUtils API
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Versions of package r-cran-rentrez |
Release | Version | Architectures |
sid | 1.2.1-2 | all |
buster | 1.2.1-2 | all |
stretch | 1.0.4-1 | all |
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License: DFSG free
|
Provides an R interface to the NCBI's EUtils API allowing users to
search databases like GenBank and PubMed, process the results of those
searches and pull data into their R sessions.
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R-cran-rocr
GNU R package to prepare and display ROC curves
|
Versions of package r-cran-rocr |
Release | Version | Architectures |
jessie | 1.0-5-1 | all |
wheezy | 1.0-4-3 | all |
squeeze | 1.0-4-1 | all |
stretch | 1.0-7-2 | all |
sid | 1.0-7-4 | all |
buster | 1.0-7-4 | all |
Debtags of package r-cran-rocr: |
field | statistics |
role | shared-lib |
use | analysing, viewing |
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License: DFSG free
|
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.
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Ruby-rgfa
parse, edit and write GFA format graphs in Ruby
|
Versions of package ruby-rgfa |
Release | Version | Architectures |
stretch | 1.3.1-1 | all |
buster | 1.3.1+dfsg-1 | all |
sid | 1.3.1+dfsg-1 | all |
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License: DFSG free
|
The Graphical Fragment Assembly (GFA) format is a proposed file format
to describe the product of a genome sequence assembly process.
rgfa implements the proposed specifications for the GFA format
described under https://github.com/pmelsted/GFA-spec/blob/master/GFA-spec.md
as closely as possible.
The library allows one to create an RGFA object from a file in the GFA format
or from scratch, to enumerate the graph elements (segments, links,
containments, paths and header lines), to traverse the graph (by
traversing all links outgoing from or incoming to a segment), to search for
elements (e.g. which links connect two segments) and to manipulate the
graph (e.g. to eliminate a link or a segment or to duplicate a segment
distributing the read counts evenly on the copies).
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Debian packages in contrib or non-free
Mgltools-networkeditor
Python GUI library for the editing of networks
|
Versions of package mgltools-networkeditor |
Release | Version | Architectures |
buster | 1.5.7-4 (non-free) | all |
jessie | 1.5.7~rc1+cvs.20140424-1 (non-free) | all |
wheezy | 1.5.6~rc3~cvs.20120206-1 (non-free) | all |
sid | 1.5.7-4 (non-free) | all |
stretch | 1.5.7-1 (non-free) | all |
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License: non-free
|
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
|
Versions of package mgltools-pybabel |
Release | Version | Architectures |
sid | 1.5.7-3 (non-free) | all |
buster | 1.5.7-3 (non-free) | all |
wheezy | 1.5.6~rc3~cvs.20120206-1 (non-free) | all |
jessie | 1.5.7~rc1+cvs.20140424-1 (non-free) | all |
stretch | 1.5.7-1 (non-free) | all |
|
License: non-free
|
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
|
Versions of package mgltools-vision |
Release | Version | Architectures |
wheezy | 1.5.6~rc3~cvs.20120601-1 (non-free) | all |
stretch | 1.5.7-1 (non-free) | all |
buster | 1.5.7+dfsg-2 (non-free) | all |
jessie | 1.5.7~rc1+cvs.20140424-1 (non-free) | all |
sid | 1.5.7+dfsg-2 (non-free) | all |
|
License: non-free
|
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.
|
Packaging has started and developers might try the packaging code in VCS
Libforester-java
Libraries for evolutionary biology and comparative genomics research
|
Versions of package libforester-java |
Release | Version | Architectures |
VCS | 0.0+20180205-1 | all |
|
License: LGPL 2.1+
Debian package not available
Version: 0.0+20180205-1
|
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,...
|
Libgoby-java
store next-generation sequencing data and intermediary analysis results
|
Versions of package libgoby-java |
Release | Version | Architectures |
VCS | 3.3.0+dfsg-1 | all |
|
License: GPL-3
Debian package not available
Version: 3.3.0+dfsg-1
|
Goby is a next-gen data management framework designed to facilitate the
implementation of efficient data analysis pipelines.
Goby provides very efficient file formats to store next-generation
sequencing data and intermediary analysis results. Goby 1.x files were
compressed with GZip. In Goby 2.0, we introduced novel compression
approaches that result in state of the art compression of alignment
data. Goby 2.0 files can compress to a few percent of a BAM file and are
often smaller than CRAM files.
Goby also provides utilities that implement common next-gen data
computations. We design these utilities to make them relatively easy to
use, yet very efficient.
|
Libqcpp-dev
C++11 library for NGS data quality control -- headers
|
Versions of package libqcpp-dev |
Release | Version | Architectures |
VCS | 0.1.9+dfsg-1 | all |
|
License: LGPL-3.0+
Debian package not available
Version: 0.1.9+dfsg-1
|
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.
|
Libroadrunner-dev
simulation engine for systems and synthetic biology (development)
|
Versions of package libroadrunner-dev |
Release | Version | Architectures |
VCS | 1.5.1-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 1.5.1-1
|
LibRoadRunner is a high performance and portable simulation engine for
systems and synthetic biology. I can run on many platforms including
Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the
original C# roadRunner developed by Frank Bergmann and Herbert Sauro.
The same original functionality however remains, including the
original C API, the structural analysis code, sensitivity and steady
state analyses, but with significant improvements to performance, back-
end design, better event handling, new C++ API and stochastic
simulation support.
This package contains the header files for libroadrunner.
Please cite:
Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat and Herbert M. Sauro:
Link
to publication
(PubMed,eprint)
Bioinformatics
31(20):3315-21
(2015)
|
Libswarm2-dev
agent-based modeling to education, biomedical research and others
|
Versions of package libswarm2-dev |
Release | Version | Architectures |
VCS | 2.4.1-1 | all |
|
License: GPL-2+
Debian package not available
Version: 2.4.1-1
|
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-roadrunner
Python bindings for libroadrunner
|
Versions of package python-roadrunner |
Release | Version | Architectures |
VCS | 1.5.1-1 | all |
|
License: Apache-2.0
Debian package not available
Version: 1.5.1-1
|
LibRoadRunner is a high performance and portable simulation engine for
systems and synthetic biology. I can run on many platforms including
Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the
original C# roadRunner developed by Frank Bergmann and Herbert Sauro.
The same original functionality however remains, including the
original C API, the structural analysis code, sensitivity and steady
state analyses, but with significant improvements to performance, back-
end design, better event handling, new C++ API and stochastic
simulation support.
This package contains the Python bindings for libroadrunner.
Please cite:
Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat and Herbert M. Sauro:
Link
to publication
(PubMed,eprint)
Bioinformatics
31(20):3315-21
(2015)
|
Python3-consensuscore2
generate consensus sequences for PacBio data -- Python 3
|
Versions of package python3-consensuscore2 |
Release | Version | Architectures |
VCS | 0.13.0+20160719-2 | all |
|
License: PacBio-BSD-3-Clause
Debian package not available
Version: 0.13.0+20160719-2
|
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-ete3
Python Environment for (phylogenetic) Tree Exploration - Python 3.X
|
Versions of package python3-ete3 |
Release | Version | Architectures |
VCS | 3.1.1+dfsg-1 | all |
|
License: GPL-3+
Debian package not available
Version: 3.1.1+dfsg-1
|
The Environment for Tree Exploration (ETE) is a Python programming
toolkit that assists in the recontruction, manipulation, analysis and
visualization of phylogenetic trees (although clustering trees or any
other tree-like data structure are also supported).
ETE is currently developed as a tool for researchers working in
phylogenetics and genomics. If you use ETE for a published work,
please cite:
Visit http://etetoolkit.org for more info.
|
Python3-misopy
Mixture of Isoforms model for RNA-Seq isoform quantitation (Python 3)
|
Versions of package python3-misopy |
Release | Version | Architectures |
VCS | 0.5.4+dfsg-1 | all |
|
License: GPL-2.0+
Debian package not available
Version: 0.5.4+dfsg-1
|
MISO (Mixture of Isoforms) is a probabilistic framework that quantitates
the expression level of alternatively spliced genes from RNA-Seq
data, and identifies differentially regulated isoforms or exons across
samples. By modeling the generative process by which reads are produced
from isoforms in RNA-Seq, the MISO model uses Bayesian inference to
compute the probability that a read originated from a particular isoform.
MISO uses the inferred assignment of reads to isoforms to quantitate the
abundances of the underlying set of alternative mRNA isoforms. Confidence
intervals over estimates can be obtained, which quantify the reliability
of the estimates.
This is the Python 3 module.
|
Python3-seqcluster
analysis of small RNA in NGS data (Python 3)
|
Versions of package python3-seqcluster |
Release | Version | Architectures |
VCS | 1.2.4~a3+git20180814.0f23886e-1 | all |
|
License: MIT
Debian package not available
Version: 1.2.4~a3+git20180814.0f23886e-1
|
Identifies small RNA sequences of all sorts
in RNA sequencing data. This is especially
helpful for the identification of RNA that
is neither coding nor belonging to the already
well-established group of miRNA, towards
many tools feel constrained to.
|
Vdjtools
post-analysis of B/T cell repertoires
|
Versions of package vdjtools |
Release | Version | Architectures |
VCS | 1.2.1-1 | all |
|
License: non-free
Debian package not available
Version: 1.2.1-1
|
VDJtools is a complementary software suite that solves a wide range of T
cell receptor (TCR) repertoires post-analysis tasks, provides a detailed
tabular output and publication-ready graphics, and is built on top of a
flexible API. Using TCR datasets for a large cohort of unrelated healthy
donors, twins, and multiple sclerosis patients we demonstrate that
VDJtools greatly facilitates the analysis and leads to sound biological
conclusions.
Please cite:
Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova and Dmitriy M. Chudakov:
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
(PubMed,eprint)
PLoS Computational Biology
11(11):e1004503
(2015)
|
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.
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|