Software Packages in "stretch", Subsection science

3depict (0.0.19-1+b1)

visualisation and analysis for single valued point data

abacas (1.3.1-3)

Algorithm Based Automatic Contiguation of Assembled Sequences

abinit (8.0.8-1+b1)

package for electronic structure calculations

abyss (2.0.2-2)

de novo, parallel, sequence assembler for short reads

acedb-other (4.9.39+dfsg.02-1)

retrieval of DNA or protein sequences

acedb-other-belvu (4.9.39+dfsg.02-1)

multiple sequence alignment editor

acedb-other-dotter (4.9.39+dfsg.02-1)

visualisation of sequence similarity

aces3 (3.0.8-5.1+b1)

Advanced Concepts in Electronic Structure III

aces3-data (3.0.8-5.1)

Advanced Concepts in Electronic Structure III

achilles (2-8.2+b1)

An artificial life and evolution simulator

adapterremoval (2.2.0-1)

rapid adapter trimming, identification, and read merging of gene sequences

adapterremoval-examples (2.2.0-1)

rapid adapter trimming, identification, and read merging (example data)

adun-core (0.81-9+b2)

Molecular Simulator

aegean (0.15.2+dfsg-1)

integrated genome analysis toolkit

aeskulap (0.2.2b1+git20161206-1)

medical image viewer and DICOM network client

aevol (4.4-1+b5 [arm64], 4.4-1+b4 [amd64, armel, armhf, i386, mips, mips64el, mipsel, ppc64el, s390x])

digital genetics model to run Evolution Experiments in silico

aghermann (1.1.2-1)

Sleep-research experiment manager

alfa (1.0-2)

Automated Line Fitting Algorithm

algotutor (0.8.6-1)

program for observing the intermediate steps of algorithm

alien-hunter (1.7-5)

Interpolated Variable Order Motifs to identify horizontally acquired DNA

altree (1.3.1-4+b2)

program to perform phylogeny-based association and localization analysis

altree-examples (1.3.1-4)

example files for ALTree

amap-align (2.2-6)

Protein multiple alignment by sequence annealing

ampliconnoise (1.29-6)

removal of noise from 454 sequenced PCR amplicons

andi (0.10-2)

Efficient Estimation of Evolutionary Distances

anfo (0.98-5)

Short Read Aligner/Mapper from MPG

ants (2.1.0-5)

advanced normalization tools for brain and image analysis

aoflagger (2.9.0-1)

Find RFI in radio astronomical observations

apbs (1.4-1+b1)

Adaptive Poisson Boltzmann Solver

apertium-af-nl (0.2.0~r58256-1)

Apertium translation data for the Afrikaans-Dutch pair

apertium-apy (0.9.1~r343-2)

Apertium APY service

apertium-arg (0.1.2~r65494-1)

Apertium single language data for Aragonese

apertium-arg-cat (0.1.0~r64925-1)

Apertium translation data for the Aragonese-Catalan pair

apertium-br-fr (0.5.0~r61325-2)

Apertium linguistic data to translate between Breton and French

apertium-ca-it (0.1.1~r57554-1)

Apertium translation data for the Catalan-Italian pair

apertium-cat (1.0.0~r65787-1)

Apertium single language data for Catalan

apertium-cy-en (0.1.1~r57554-3)

Apertium translation data for the Welsh-English pair

apertium-dan (0.5.0~r67099-1)

Apertium single language data for Danish

apertium-dan-nor (1.3.0~r67099-1)

Apertium translation data for the Danish-Norwegian pair

apertium-dev (3.4.0~r61013-5+b1)

Development tools and library for Apertium

apertium-en-gl (0.5.2~r57551-1)

Apertium translation data for the English-Galician pair

apertium-eo-en (1.0.0~r63833-1)

Apertium linguistic data to translate between Esperanto and English

apertium-eo-fr (0.9.0~r57551-1)

Apertium translation data for the Esperanto-French pair

apertium-es-ast (1.1.0~r51165-1)

Apertium translation data for the Spanish-Asturian pair

apertium-es-it (0.1.0~r51165-1)

Apertium translation data for the Spanish-Italian pair

apertium-eu-en (0.3.1~r56205-1)

Apertium translation data for the Basque-English pair

apertium-fra (1.0.0~r65786-1)

Apertium single language data for French

apertium-fra-cat (1.1.0~r64309-1)

Apertium translation data for the French-Catalan pair

apertium-hbs (0.5.0~r68212-2)

Apertium single language data for Serbo-Croatian

apertium-hbs-eng (0.1.0~r57598-1)

Apertium translation data for the Serbo-Croatian - English pair

apertium-hbs-mkd (0.1.0~r57554-1)

Apertium translation data for the Serbo-Croatian-Macedonian pair

apertium-hbs-slv (0.1.0~r59294-1)

Apertium translation data for the Serbo-Croatian-Slovenian pair

apertium-hin (0.1.0~r59158-1)

Apertium single language data for Hindi

apertium-id-ms (0.1.1~r57551-1)

Apertium translation data for the Indonesian-Malay pair

apertium-is-sv (0.1.0~r56030-1)

Apertium translation data for the Icelandic-Swedish pair

apertium-isl (0.1.0~r65494-1)

Apertium single language data for Icelandic

apertium-isl-eng (0.1.0~r66083-1)

Apertium translation data for the Icelandic-English pair

apertium-ita (0.9.0~r72553-1)

Apertium single language data for Italian

apertium-kaz (0.1.0~r61338-1)

Apertium single language data for Kazakh

apertium-kaz-tat (0.2.1~r57554-1)

Apertium translation data for the Kazakh-Tatar pair

apertium-lex-tools (0.1.1~r66150-1+b1)

Constraint-based lexical selection module

apertium-mk-bg (0.2.0~r49489-1)

Apertium translation data for the Macedonian-Bulgarian pair

apertium-mk-en (0.1.1~r57554-1)

Apertium translation data for the Macedonian-English pair

apertium-mlt-ara (0.2.0~r62623-1)

Apertium translation data for the Maltese-Arabic pair

apertium-nno (0.9.0~r69513-1)

Apertium single language data for Norwegian Nynorsk

apertium-nno-nob (1.1.0~r66076-1)

Apertium translation data for the Norwegian Nynorsk-Norwegian Bokmål pair

apertium-nob (0.9.0~r69513-1)

Apertium single language data for Norwegian Bokmål

apertium-sme-nob (0.6.0~r61921-1)

Apertium translation data for the Northern Sami-Norwegian Bokmål pair

apertium-spa (0.1.0~r65494-1)

Apertium single language data for Spanish

apertium-spa-arg (0.4.0~r64399-1)

Apertium translation data for the Spanish-Aragonese pair

apertium-srd (0.9.0~r72792-1)

Apertium single language data for Sardinian

apertium-srd-ita (0.9.0~r72554-1)

Apertium translation data for the Sardinian-Italian pair

apertium-swe (0.7.0~r69513-1)

Apertium single language data for Swedish

apertium-swe-dan (0.7.0~r66063-1)

Apertium translation data for the Swedish-Danish pair

apertium-tat (0.1.0~r60887-1)

Apertium single language data for Tatar

apertium-urd (0.1.0~r61311-1)

Apertium single language data for Urdu

apertium-urd-hin (0.1.0~r64379-1)

Apertium translation data for the Urdu-Hindi pair

aragorn (1.2.38-1)

tRNA and tmRNA detection in nucleotide sequences

arb (6.0.6-1) [non-free]

phylogenetic sequence analysis suite - main program

arb-common (6.0.6-1) [non-free]

phylogenetic sequence analysis suite - common files

arden (1.0-3)

specificity control for read alignments using an artificial reference

ariba (2.6.1+ds-1)

Antibiotic Resistance Identification By Assembly

art-nextgen-simulation-tools (20160605+dfsg-2)

simulation tools to generate synthetic next-generation sequencing reads

art-nextgen-simulation-tools-profiles (20160605+dfsg-2)

profiles for art simulation tools

artemis (16.0.17+dfsg-1)

genome browser and annotation tool

artfastqgenerator (0.0.20150519-2)

outputs artificial FASTQ files derived from a reference genome

artfastqgenerator-examples (0.0.20150519-2)

ou7puts artificial FASTQ files derived from a reference genome (examples)

asdftool (1.2.1-2)

Command line tool to manipulate ASDF scientific data files

ask (1.1.1-1)

Adaptive Sampling Kit for big experimental spaces

astro-tasks (1.0)

Debian Astronomy Pure Blend (tasksel tasks)

astromatic (1.1)

Astronomical pipeline software collection

astrometry-data-2mass (1.1) [contrib]

Astrometry.net 2MASS index files downloader

astrometry-data-2mass-00 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (2'-2.8')

astrometry-data-2mass-01 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (2.8'-4')

astrometry-data-2mass-02 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (4'-5.6')

astrometry-data-2mass-03 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (5.6'-8')

astrometry-data-2mass-04 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (8'-11')

astrometry-data-2mass-05 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (11'-16')

astrometry-data-2mass-06 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (16'-22')

astrometry-data-2mass-07 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (22'-30')

astrometry-data-2mass-08-19 (1.1) [contrib]

Astrometry.net 2MASS index files downloader (30'-2000')

astrometry-data-tycho2 (2-3)

Astrometry.net Tycho-2 index files

astrometry-data-tycho2-07 (2-3)

Astrometry.net Tycho-2 index files (22'-30')

astrometry-data-tycho2-07-bigendian (2-3)

Astrometry.net Tycho-2 big endian index files (22'-30')

astrometry-data-tycho2-07-littleendian (2-3)

Astrometry.net Tycho-2 little endian index files (22'-30')

astrometry-data-tycho2-08 (2-3)

Astrometry.net Tycho-2 index files (30'-44')

astrometry-data-tycho2-08-bigendian (2-3)

Astrometry.net Tycho-2 big endian index files (30'-44')

astrometry-data-tycho2-08-littleendian (2-3)

Astrometry.net Tycho-2 little endian index files (30'-44')

astrometry-data-tycho2-09 (2-3)

Astrometry.net Tycho-2 index files (44'-60')

astrometry-data-tycho2-09-bigendian (2-3)

Astrometry.net Tycho-2 big endian index files (44'-60')

astrometry-data-tycho2-09-littleendian (2-3)

Astrometry.net Tycho-2 little endian index files (44'-60')

astrometry-data-tycho2-10-19 (2-3)

Astrometry.net Tycho-2 index files (60'-2000')

astrometry-data-tycho2-10-19-bigendian (2-3)

Astrometry.net Tycho-2 big endian index files (60'-2000')

astrometry-data-tycho2-10-19-littleendian (2-3)

Astrometry.net Tycho-2 little endian index files (60'-2000')

astrometry.net (0.70+dfsg-1)

Astrometry plate solver

astronomical-almanac (5.6-4+b2)

astronomical almanac - calculate planet and star positions

astropy-utils (1.3-8)

Command line tools from astropy

atac (0~20150903+r2013-3)

genome assembly-to-assembly comparison

augustus (3.2.3+dfsg-1)

gene prediction in eukaryotic genomes

augustus-data (3.2.3+dfsg-1)

data files for AUGUSTUS

autodock (4.2.6-3+b1)

analysis of ligand binding to protein structure

autodock-getdata (4.2.6-3)

instructions for getData to collect compounds

autodock-test (4.2.6-3)

test files for AutoDock

autodock-vina (1.1.2-3+b6 [amd64], 1.1.2-3+b5 [armel, armhf, i386, mips, mipsel, s390x], 1.1.2-3+b4 [arm64, ppc64el], 1.1.2-3+b2 [mips64el])

docking of small molecules to proteins

autogrid (4.2.6-3+b1)

pre-calculate binding of ligands to their receptor

autogrid-test (4.2.6-3)

test files for AutoGrid

avce00 (2.0.0-5)

Conversion of ESRI Arcinfo Vector Coverage in E00 format

avogadro (1.2.0-1+deb9u1)

Molecular Graphics and Modelling System

avogadro-data (1.2.0-1+deb9u1)

Molecular Graphics and Modelling System (Data Files)

aweather (0.8.1-1.1)

Advanced Weather Monitoring Program

axe-demultiplexer (0.3.2+dfsg1-1)

Trie-based DNA sequencing read demultiplexer

bagel (0.0~git20170109-1)

Computational Chemistry Package

bagel-data (0.0~git20170109-1)

Computational Chemistry Package (data files)

ballview (1.4.3~beta1-3)

free molecular modeling and molecular graphics tool

bamtools (2.4.1+dfsg-1)

toolkit for manipulating BAM (genome alignment) files

barrnap (0.7+dfsg-2)

rapid ribosomal RNA prediction

bart (0.4.00-1)

tools for computational magnetic resonance imaging

bauble (0.9.7-2.1)

biodiversity collection manager software application

bcftools (1.3.1-1+b1)

genomic variant calling and manipulation of VCF/BCF files

beagle (4.1~160727-86a+dfsg-1)

Genotype calling, genotype phasing and imputation of ungenotyped markers

beast-mcmc (1.8.4+dfsg.1-1)

Bayesian MCMC phylogenetic inference

beast2-mcmc (2.4.4+dfsg-1)

Bayesian MCMC phylogenetic inference

bedtools (2.26.0+dfsg-3)

suite of utilities for comparing genomic features

bedtools-test (2.26.0+dfsg-3)

test data for the bedtools package

berkeley-express (1.5.1-3+b1)

Streaming quantification for high-throughput sequencing

bibus (1.5.2-4)

bibliographic database

bio-eagle (2.3-3)

Haplotype phasing within a genotyped cohort or using a phased reference panel

bio-eagle-examples (2.3-3)

Examples for bio-eagle

bio-rainbow (2.0.4-1+b1)

clustering and assembling short reads for bioinformatics

biogenesis (0.8-2)

artificial life program that simulates evolution of organisms

biomaj (1.2.3-11)

biological data-bank updater

biomaj-properties (1.2.3-11)

biological data-bank updater - example properties files

biomaj-watcher (1.2.2-4) [contrib]

biological data-bank updater - web interface

bioperl (1.7.1-2)

Perl tools for computational molecular biology

bioperl-run (1.7.1-3)

BioPerl wrappers: scripts

biosig-tools (1.3.0-2.2)

format conversion tools for biomedical data formats

biosquid (1.9g+cvs20050121-7)

utilities for biological sequence analysis

bist (0.5.2-1.1+b1)

chemical drawing tool

bkchem (0.13.0-5)

Chemical structures editor

blasr (5.3+0-1)

mapping single-molecule sequencing reads

blast2 (1:2.6.0-1)

transitional dummy package to ncbi-blast+-legacy

blimps-utils (3.9-1) [non-free]

blocks database improved searcher

bmt (0.6-1)

software analysis benchmarking toolkit

bodr (10-1)

Blue Obelisk Data Repository

boinc-app-seti (8.00~svn3363-3)

SETI@home application for the BOINC client

boinc-app-seti-graphics (8.00~svn3363-3)

SETI@home application for the BOINC client (with graphics)

boolector (1.5.118.6b56be4.121013-1+b1)

SMT solver for bit-vectors and arrays

bowtie (1.1.2-6)

Ultrafast memory-efficient short read aligner

bowtie-examples (1.1.2-6)

Examples for bowtie, the ultrafast memory-efficient short read aligner

bowtie2 (2.3.0-2)

ultrafast memory-efficient short read aligner

bowtie2-examples (2.3.0-2)

Examples for bowtie2

boxshade (3.3.1-10)

Pretty-printing of multiple sequence alignments

bppphyview (0.3.0-1.1+b1)

Bio++ Phylogenetic Viewer

bppsuite (2.2.0-0.1+b1)

Bio++ program suite

brig (0.95+dfsg-1)

BLAST Ring Image Generator

bwa (0.7.15-2)

Burrows-Wheeler Aligner

cafeobj (1.5.5-1+b1)

new generation algebraic specification and programming language

cafeobj-mode (1.5.5-1)

Emacs major mode for editing CafeOBJ source code

caffe-cpu (1.0.0~rc4-1)

Fast, open framework for Deep Learning (Meta)

caffe-tools-cpu (1.0.0~rc4-1)

Tools for fast, open framework for Deep Learning (CPU_ONLY)

caffe-tools-cuda (1.0.0~rc4-1) [contrib]

Tools for fast, open framework for Deep Learning (CUDA)

cain (1.10+dfsg-2)

simulations of chemical reactions

cain-examples (1.10+dfsg-2)

examples for cain

cain-solvers (1.10+dfsg-2)

solvers for cain

calculix-ccx (2.11-1+b1)

Three-Dimensional Structural Finite Element Program

calculix-cgx (2.11+dfsg-1+b1)

Calculix cgx is a 3-dimensional pre- and post-processor for fem

camitk-actionstatemachine (4.0.4-2)

pipeline replay application for the CamiTK library

camitk-config (4.0.4-2)

Computer Assisted Medical Intervention Tool Kit - config

camitk-imp (4.0.4-2)

workbench application for the CamiTK library

casacore-data-igrf (10-1)

International Geomagnetic Reference Field data for casacore

casacore-data-lines (0+git2016.11.26-2)

Table of spectral line frequencies for casacore

casacore-data-observatories (0+git2016.11.02-1)

Table of radio observatory coordinates for casacore

casacore-data-sources (2-2)

Table of ICRF reference source coordinates for casacore

casacore-data-tai-utc (1.1)

Difference table between TAI and UTC for casacore

casacore-tools (2.2.0-2)

Tools built with CASA

cassbeam (1.1-1+b1)

Cassegrain antenna modelling

cassiopee (1.0.5-1+b1 [amd64], 1.0.5-1 [arm64, armel, armhf, i386, mips, mips64el, mipsel, ppc64el, s390x])

index and search tool in genomic sequences

cba (0.3.6-4.1+b2)

Continuous Beam Analysis

cbflib-bin (0.9.2.2-1+b1)

utilities to manipulate CBF files

cbmc (5.6-1)

bounded model checker for C and C++ programs

cclib (1.3.1-1)

Parsers and algorithms for computational chemistry

cclib-data (1.1-1) [non-free]

Parsers and algorithms for computational chemistry (data files)

cd-hit (4.6.6-2)

suite of programs designed to quickly group sequences

cdbfasta (0.99-20100722-3)

Constant DataBase indexing and retrieval tools for multi-FASTA files

cernlib (20061220+dfsg3-4.3)

CERNLIB data analysis suite - general use metapackage

cernlib-core (20061220+dfsg3-4.3)

CERNLIB data analysis suite - main libraries and programs

cernlib-extras (20061220+dfsg3-4.3)

CERNLIB data analysis suite - extra programs

cernlib-montecarlo (20061220+dfsg3-3.1)

CERNLIB Monte Carlo libraries

cg3 (0.9.9~r11624-1+b3)

Tools for using the 3rd edition of Constraint Grammar (CG-3)

cgns-convert (3.3.0-4)

CFD General Notation System - Conversion tools

cgview (0.0.20100111-2)

Circular Genome Viewer

ch5m3d (1.2.5+dfsg-1)

create and visualize 3-dimensional drawings of simple molecules

chemical-structures (2.2.dfsg.0-12)

set of molecular structures in open formats

chemps2 (1.8.3-2)

Executable to call libchemps2-2 from the command line

chemtool (1.6.14-1+b1)

chemical structures drawing program

chimeraslayer (20101212+dfsg1-1)

detects likely chimeras in PCR amplified DNA

circlator (1.4.1-1)

circularize genome assemblies

circos (0.69.4+dfsg-1)

plotter for visualizing data

circos-tools (0.22-1)

plotter for visualizing data - helper utilities

ckon (0.7.1-3+b3 [amd64, arm64, armel, armhf, i386, mips, mipsel, ppc64el, s390x], 0.7.1-3+b2 [mips64el])

automatic build tool for ROOT data analysis software

clearcut (1.0.9-1+b1)

extremely efficient phylogenetic tree reconstruction

clonalframe (1.2-5)

inference of bacterial microevolution using multilocus sequence data

clustalo (1.2.4-1)

General purpose multiple sequence alignment program for proteins

clustalw (2.1+lgpl-5)

global multiple nucleotide or peptide sequence alignment

clustalx (2.1+lgpl-5)

Multiple alignment of nucleic acid and protein sequences (graphical interface)

cluster3 (1.52a-1) [non-free]

Reimplementation of the Eisen-clustering software

cmor-tables (3.2-1)

MIP tables for the Climate Model Output Rewriter library

cmtk (3.3.1-1.1)

Computational Morphometry Toolkit

code-aster-gui (1.13.1-2)

Graphical user interface for Code_Aster - client

code-aster-run (1.13.1-2)

Graphical user interface for Code_Aster - server

code-saturne (4.3.3+repack-1)

General purpose Computational Fluid Dynamics (CFD) software

code-saturne-bin (4.3.3+repack-1)

General purpose Computational Fluid Dynamics (CFD) software - binaries

code-saturne-data (4.3.3+repack-1)

General purpose Computational Fluid Dynamics (CFD) software - data

code-saturne-doc (4.3.3+repack-1)

General purpose Computational Fluid Dynamics (CFD) software - Documentation

code-saturne-include (4.3.3+repack-1)

General purpose Computational Fluid Dynamics (CFD) software - includes

codonw (1.4.4-3+b1)

Correspondence Analysis of Codon Usage

coinor-cbc (2.8.12-1+b2)

Coin-or branch-and-cut mixed integer programming solver

coinor-clp (1.15.10-3+b1)

Coin-or linear programming solver

coinor-csdp (6.1.1-1+b2)

A software package for semidefinite programming

coinor-libcbc3 (2.8.12-1+b2)

Coin-or branch-and-cut mixed integer programming solver (shared libraries)

coinor-libcgl1 (0.58.9-1+b1 [amd64, arm64, armel, armhf, i386, mips, mipsel, ppc64el, s390x], 0.58.9-1 [mips64el])

COIN-OR Cut Generation Library

coinor-libclp1 (1.15.10-3+b1)

Coin-or linear programming solver (shared libraries)

coinor-libcoinutils3v5 (2.9.15-4)

Coin-or collection of utility classes (binaries and libraries)

coinor-libflopc++0 (1.0.6-3.1+b2 [amd64, armel, armhf, i386, mips, mipsel, s390x], 1.0.6-3.1+b1 [ppc64el], 1.0.6-3.1 [arm64, mips64el])

Formulation of Linear Optimization Problems in C++

coinor-libosi1v5 (0.106.9-2+b1)

COIN-OR Open Solver Interface

coinor-libsymphony3 (5.6.1-1+b2)

COIN-OR solver for mixed-integer linear programs (shared libraries)

coinor-symphony (5.6.1-1+b2)

COIN-OR solver for mixed-integer linear programs

comet-ms (2014022-3+b2)

Tandem mass spectrometry (MS/MS) search engine

concavity (0.1+dfsg.1-1)

predictor of protein ligand binding sites from structure and conservation

connectome-workbench (1.2.3+git3-g7b83782-1)

brain visualization, analysis and discovery tool

conservation-code (20110309.0-5)

protein sequence conservation scoring tool

cp2k (4.1-1+b1)

Ab Initio Molecular Dynamics

cp2k-data (4.1-1)

Ab Initio Molecular Dynamics (data files)

cpl-plugin-amber (4.3.4+dfsg-1+b1)

ESO data reduction pipeline for the AMBER instrument

cpl-plugin-amber-calib (4.3.4+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for AMBER

cpl-plugin-fors (5.3.11+dfsg-1)

ESO data reduction pipeline for the FORS1/2 instruments

cpl-plugin-fors-calib (5.3.11+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for FORS2

cpl-plugin-giraf (2.15+dfsg-1+b1)

ESO data reduction pipeline for the GIRAFFE instrument

cpl-plugin-giraf-calib (2.15+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for GIRAFFE

cpl-plugin-hawki (1.8.21+dfsg-1)

ESO data reduction pipeline for the HAWK-I instrument

cpl-plugin-hawki-calib (1.8.21+dfsg-1)

ESO data reduction pipeline calibration data downloader for HAWK-I

cpl-plugin-kmos (1.4.0+dfsg-1)

ESO data reduction pipeline for the KMOS instrument

cpl-plugin-kmos-calib (1.4.0+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for KMOS

cpl-plugin-muse (1.6.2+dfsg-1)

ESO data reduction pipeline for the MUSE instrument

cpl-plugin-muse-calib (1.6.2+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for MUSE

cpl-plugin-naco (4.4.1+dfsg-3)

ESO data reduction pipeline for the NaCo instrument

cpl-plugin-naco-calib (4.4.1+dfsg-3) [contrib]

ESO data reduction pipeline NaCo calibration data downloader

cpl-plugin-uves (5.7.0+dfsg-1+b1)

ESO data reduction pipeline for the UVES instrument

cpl-plugin-uves-calib (5.7.0+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for UVES

cpl-plugin-vimos (3.1.7+dfsg-1+b1)

ESO data reduction pipeline for the VIMOS instrument

cpl-plugin-vimos-calib (3.1.7+dfsg-1) [contrib]

ESO data reduction pipeline calibration data downloader for VIMOS

cpl-plugin-visir (4.3.0+dfsg1-1+b1)

ESO data reduction pipeline for the VISIR instrument

cpl-plugin-visir-calib (4.3.0+dfsg1-1) [contrib]

ESO data reduction pipeline calibration data downloader for VISIR

cpl-plugin-xshoo (2.8.4+dfsg-3)

ESO data reduction pipeline for the XSHOOTER instrument

cpl-plugin-xshoo-calib (2.8.4+dfsg-3) [contrib]

ESO data reduction pipeline calibration data downloader for XSHOOTER

crac (2.5.0+dfsg-1)

integrated RNA-Seq read analysis

critterding (1.0-beta12.1-1.3+b1)

Evolving Artificial Life

ctsim (5.2.0-4)

Computed tomography simulator

ctsim-help (5.2.0-4)

Online help file for CTSim

cufflinks (2.2.1-3+b1) [non-free]

Transcript assembly, differential expression and regulation for RNA-Seq

cutadapt (1.12-2)

Clean biological sequences from high-throughput sequencing reads

cwltool (1.0.20170114120503-1)

Common workflow language reference implementation

daligner (1.0+20161119-1)

local alignment discovery between long nucleotide sequencing reads

dans-gdal-scripts (0.24-1+b1)

GDAL contributed tools by Geographic Information Network of Alaska

dascrubber (0~20160601-2)

alignment-based scrubbing pipeline for DNA sequencing reads

datalad (0.4.1-1)

data files crawler and data distribution

dawg (1.2-1+b1)

program to simulate the evolution of recombinant DNA sequences

dazzdb (1.0+20161112-2)

manage nucleotide sequencing read data

dcm2niix (1.0.20161101-1)

next generation DICOM to NIfTI converter

dcmtk (3.6.1~20160216-4)

OFFIS DICOM toolkit command line utilities

debian-astro-logo (1.0)

Debian Astronomy Pure Blends Logo

dh-r (20161219)

Debian helper tools for packaging R libraries

dialign (2.2.1-8)

Segment-based multiple sequence alignment

dialign-tx (1.0.2-9)

Segment-based multiple sequence alignment

dialign-tx-data (1.0.2-9)

Segment-based multiple sequence alignment (data files)

dicomnifti (2.32.1-1+b1)

converts DICOM files into the NIfTI format

dicompyler (0.4.2-3)

radiation therapy research platform

dimbl (0.15-1)

Distributed Memory Based Learner

dindel (1.01+dfsg-4+b1)

determines indel calls from short-read data

discosnp (1.2.6-1+b2)

discovering Single Nucleotide Polymorphism from raw set(s) of reads

disulfinder (1.2.11-6)

cysteines disulfide bonding state and connectivity predictor

disulfinder-data (1.2.11-6)

data files for predictor of disulfide bonds in proteins

dnaclust (3-4+b2)

tool for clustering millions of short DNA sequences

doris (4.06~beta2+dfsg-3+b1) [contrib]

Delft object-oriented radar interferometric software

dozzaqueux (3.50-1+b1)

simulator for chemical mixtures

dozzaqueux-data (3.50-1)

databases for chemical mixtures

dpuser (3.3+p1+dfsg-2)

Interactive language for handling numbers, strings, and matrices

drawxtl (5.5-3+b2)

crystal structure viewer

drslib (0.3.0a3-5)

Command-line tools for the Data Reference Syntax library

dsdp (5.8-9.4)

Software for Semidefinite Programming

dssp (2.2.1-3+b2)

protein secondary structure assignment based on 3D structure

dwgsim (0.1.11-3+b1)

short sequencing read simulator

dx (1:4.4.4-9+b1)

OpenDX (IBM Visualization Data Explorer) - main package

dxsamples (4.4.0-3)

Sample programs for the OpenDX Data Explorer

e00compr (1.0.1-3)

Program to read/write Arcinfo compressed E00 files

ea-utils (1.1.2+dfsg-4)

command-line tools for processing biological sequencing data

easychem (0.6-8+b1)

Draw high-quality molecules and 2D chemical formulas

ecaccess (4.0.1-1)

clients to access ECMWF facilities

ecopcr (0.5.0+dfsg-1)

estimate PCR barcode primers quality

edfbrowser (1.58-1+b1)

viewer for biosignal storage files such as bdf and edf

edtsurf (0.2009-4+b1 [amd64], 0.2009-4 [arm64, armel, armhf, i386, mips, mips64el, mipsel, ppc64el, s390x])

triangulated mesh surfaces for protein structures

eficas (6.4.0-1-1.2)

Graphical editor for Code Aster command files

eigensoft (6.1.4+dfsg-1+b1)

reduction of population bias for genetic analyses

elastix (4.8-10+b1)

toolbox for rigid and nonrigid registration of images

elk-lapw (4.0.15-2+b1)

All-Electron Density-Functional Electronic Structure Code

elki (0.7.1-3)

Data mining algorithm development framework

elki-dev (0.7.1-3)

Data mining algorithm development framework - development files

embassy-domainatrix (0.1.660-1)

Extra EMBOSS commands to handle domain classification file

embassy-domalign (0.1.660-1)

Extra EMBOSS commands for protein domain alignment

embassy-domsearch (1:0.1.660-1)

Extra EMBOSS commands to search for protein domains

embassy-phylip (3.69.660-1) [non-free]

EMBOSS conversions of the programs in the phylip package

emboss (6.6.0+dfsg-6)

European molecular biology open software suite

emboss-data (6.6.0+dfsg-6)

data files for the EMBOSS package

emboss-explorer (2.2.0-8)

web-based GUI to EMBOSS

emboss-lib (6.6.0+dfsg-6)

EMBOSS Libraries

engauge-digitizer (9.7+ds.1-1)

interactively extracts numbers from bitmap graphs or maps

ent (1.2debian-1+b1)

pseudorandom number sequence test program

epigrass (2.4.7-1)

scientific tool for simulations and scenario analysis in network epidemiology

epsilon-bin (0.9.2+dfsg-2)

Library for wavelet image compression - tools

ergo (3.5-1+b1)

Quantum chemistry program for large-scale calculations

eso-midas (15.09pl1.0-2+b2)

European Southern Observatory Munich Image Data Analysis System

eso-pipelines (1.2)

ESO VLT Instrument pipeline collection

esorex (3.12.3-1+b2)

Execution Tool for European Southern Observatory pipelines

esys-particle (2.3.4+dfsg1-4)

Software for particle-based numerical modelling. MPI version.

etsf-io (1.0.4-1.1+b1)

Binary tools to check, merge and read ETSF files

exonerate (2.4.0-2)

generic tool for pairwise sequence comparison

expeyes (4.2.1+dfsg-1)

hardware & software framework for developing science experiments

expeyes-clib (4.2.1+dfsg-1)

hardware & software framework for developing science experiments

falcon (1.8.6-1.1)

diploid-aware genome assembly of single-molecule sequencing reads

fastahack (0.0+20160702-1+b1)

utility for indexing and sequence extraction from FASTA files

fastaq (3.14.0-1)

FASTA and FASTQ file manipulation tools

fastdnaml (1.2.2-11+b1)

Tool for construction of phylogenetic trees of DNA sequences

fastlink (4.1P-fix100+dfsg-1+b1)

faster version of pedigree programs of Linkage

fastml (3.1-3)

maximum likelihood ancestral amino-acid sequence reconstruction

fastqc (0.11.5+dfsg-6)

quality control for high throughput sequence data

fastqtl (2.184+dfsg-5)

Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes

fasttree (2.1.9-1)

phylogenetic trees from alignments of nucleotide or protein sequences

fastx-toolkit (0.0.14-3)

FASTQ/A short nucleotide reads pre-processing tools

fcc (2.8-1+b1)

Script to compile C/C++ programs and link to Fortran libraries

feedgnuplot (1.40-1)

Pipe-oriented frontend to Gnuplot

ffindex (0.9.9.7-3)

simple index/database for huge amounts of small files

figtree (1.4.2+dfsg-2)

graphical phylogenetic tree viewer

filo (1.1.0-3+b1)

FILe and stream Operations

fitgcp (0.0.20150429-1)

fitting genome coverage distributions with mixture models

fitscut (1.4.4-4+b3)

Extract cutouts from FITS image format files

fitsh (0.9.2-1+b1)

Software package for astronomical image processing

fitspng (0.3.5-1+b1)

FITS to PNG converter

fitsverify (4.18-1+b1)

FITS File Format-Verification Tool

fityk (1.3.0-1)

general-purpose nonlinear curve fitting and data analysis

flexbar (2.50-2+b1)

flexible barcode and adapter removal for sequencing platforms

flextra (5.0-6)

Trajectory model for tracing air transport phenomena

fml-asm (0.1-2+b1)

tool for assembling Illumina short reads in small regions

foma-bin (0.9.18+r243-1+b2)

Xerox-compatible finite-state compiler - library

form (4.1-1)

Symbolic manipulation system

fractalnow (0.8.1-1.1+b1)

Fast, advanced fractal generator

free42-nologo (1.4.77-1.2)

Free42 is a re-implementation of the HP-42S calculator

freecad (0.16+dfsg2-3)

Extensible Open Source CAx program (alpha)

freecontact (1.0.21-5)

fast protein contact predictor

freediams (0.9.4-1+b1)

pharmaceutical drug prescription and interaction manager

freemedforms-common-resources (0.9.4-1)

common data for the FreeMedForms project applications

freemedforms-emr (0.9.4-1+b1)

electronic medical record manager

freemedforms-emr-resources (0.9.4-1)

data for the FreeMedForms EMR

freemedforms-freedata (0.9.4-1)

free extra-data for the FreeMedForms project

freemedforms-libs (0.9.4-1+b1)

common libs for the FreeMedForms project

freemedforms-project (0.9.4-1)

FreeMedForms project

freemedforms-theme (0.9.4-1)

theme for the FreeMedForms project

frog (0.13.7-1)

tagger and parser for natural languages (runtime)

frogdata (0.13-1)

Data files for Frog

fsa (1.15.9+dfsg-3)

Fast Statistical Alignment of protein, RNA or DNA sequences

fsm-lite (1.0-2)

frequency-based string mining (lite)

ftools-fv (5.4+dfsg-2)

Tool for viewing and editing FITS format files

ftools-pow (5.4+dfsg-2+b1)

Curve plotting and image display interface tool

funtools (1.4.7-1)

Minimal buy-in FITS utility package

fxt-tools (0.3.2-2+b1)

Multithreaded tracing library

g3data (1:1.5.3-2.1+b1)

extract data from scanned graphs

gabedit (2.4.8-3+b1)

graphical user interface to Ab Initio packages

galileo (0.5.1-4)

Utility to securely synchronize a Fitbit device with the Fitbit web service

galileo-daemon (0.5.1-4)

Utility to securely synchronize a Fitbit device - daemon

gamgi (0.17.1-1+b1)

General Atomistic Modelling Graphic Interface (GAMGI)

gamgi-data (0.17.1-1)

General Atomistic Modelling Graphic Interface (data)

garli (2.1-1)

phylogenetic analysis of molecular sequence data using maximum-likelihood

garli-examples (2.1-1)

phylogenetic analysis of molecular sequence data using maximum-likelihood (examples)

garlic (1.6-1.1+b2)

A visualization program for biomolecules

gasic (0.0.r19-1)

genome abundance similarity correction

gausssum (3.0.1.1-1)

parse and display Gaussian, GAMESS, and etc's output

gazebo7 (7.3.1+dfsg-3)

Open Source Robotics Simulator - Binaries

gazebo7-common (7.3.1+dfsg-3)

Open Source Robotics Simulator - Shared files

gazebo7-plugin-base (7.3.1+dfsg-3)

Open Source Robotics Simulator - base plug-ins

gbrowse (2.56+dfsg-2)

GMOD Generic Genome Browser

gbrowse-calign (2.56+dfsg-2)

CAlign helper

gbrowse-data (2.56+dfsg-2)

Sample data to use GBrowse

gbutils (5.6.8-1+b1)

utilities for command line econometrics

gchempaint (0.14.15-1)

2D chemical structures editor for the GNOME2 desktop

gcrystal (0.14.15-1)

lightweight crystal structures visualizer

gcu-bin (0.14.15-1)

GNOME chemistry utils (helper applications)

gcu-plugin (0.14.15-1)

GNOME chemistry utils (browser plugin)

gcx (1.3-1.1+b2)

astronomical image processing and photometry gtk+ application

gdal-bin (2.1.2+dfsg-5)

Geospatial Data Abstraction Library - Utility programs

gdis (0.90-5+b1)

molecular and crystal model viewer

gdis-data (0.90-5)

molecular and crystal model viewer (data files)

gdl-astrolib (2016.11.10+dfsg-1)

Low-level astronomy software for GDL

gdl-coyote (2016.11.13-1)

GDL library from D. Fannings IDL courses

gdl-mpfit (1.84+2016.05.19-1)

Robust non-linear least squares curve fitting for GDL

gdpc (2.2.5-6)

visualiser of molecular dynamic simulations

gdpc-examples (2.2.5-6)

example files for the gdpc program

geant321 (1:3.21.14.dfsg-11)

[Physics] Particle detector description and simulation tool

geant321-data (1:3.21.14.dfsg-11)

[Physics] Data for GEANT 3.21 detector simulator

gelemental (1.2.0-10+b1)

Periodic Table viewer

genometools (1.5.9+ds-4)

versatile genome analysis toolkit

genometools-common (1.5.9+ds-4)

shared data files for GenomeTools

gentle (1.9+cvs20100605+dfsg1-5)

suite to plan genetic cloning

geographiclib-tools (1.46-2+b1)

C++ library to solve some geodesic problems -- tools

geotiff-bin (1.4.2-2+b1)

GeoTIFF (geografic enabled TIFF) library -- tools

gerris (20131206+dfsg-17)

Fluid Flow Solver

getdata (0.2-1)

management of external databases

gff2aplot (2.0-8+b1)

pair-wise alignment-plots for genomic sequences in PostScript

gff2ps (0.98d-5)

produces PostScript graphical output from GFF-files

gfsview (20121130+dfsg-4)

graphical viewer for Gerris simulation files

gfsview-batch (20121130+dfsg-4)

batch-version of viewer for Gerris simulation files

ghkl (5.0.0.2173-2)

diffractometer computation control application

giella-core (0.1.1~r129227+svn121148-1)

GTCORE files for building Giellatekno language packages

giella-sme (0.0.20150917~r121176-1)

Giellatekno single language data for North Saami

giella-sme-dev (0.0.20150917~r121176-1)

Giellatekno single language data for North Saami (dev extras)

giira (0.0.20140625-1)

RNA-Seq driven gene finding incorporating ambiguous reads

ginga (2.6.1-2)

Astronomical image viewer

ginkgocadx (3.8.4-1)

Medical Imaging Software and complete DICOM Viewer

glam2 (1064-3+b1)

gapped protein motifs from unaligned sequences

gliese (3.0.95-2) [non-free]

stellar data set from the Third Catalogue of Nearby Stars

glueviz (0.9.1+dfsg-1)

Linked data visualization

gmap (2017-01-14-1) [non-free]

spliced and SNP-tolerant alignment for mRNA and short reads

gmt (5.3.1+dfsg-2+b1)

Generic Mapping Tools

gmt-common (5.3.1+dfsg-2)

Generic Mapping Tools - Architecture-independent files

gmt-dcw (1.1.2-2)

Digital Chart of the World (DCW) for GMT

gmt-gshhg (2.3.6-2)

Global Self-consistent Hierarchical High-resolution Geography (GSHHG)

gmt-gshhg-full (2.3.6-2)

Full resolution coastlines for the Generic Mapping Tools

gmt-gshhg-high (2.3.6-2)

High resolution coastlines for the Generic Mapping Tools

gmt-gshhg-low (2.3.6-2)

Low resolution coastlines for the Generic Mapping Tools

gnuastro (0.2.33-1)

GNU Astronomy Utilities programs

gpaw (1.1.0-1+b2)

DFT and beyond within the projector-augmented wave method

gpaw-data (0.9.20000-1)

gpaw datasets/setups

gperiodic (2.0.10-7+b1)

periodic table application

gpx (2.5.2-1+b1)

Gcode to x3g conversion post processor

gpx2shp (0.71.0-4+b1)

convert GPS or GPX file to ESRI Shape file

gr-fcdproplus (3.7.25.4b6464b-2+b2)

Funcube Dongle Pro Plus controller for GNU Radio

graphlan (1.1-2)

circular representations of taxonomic and phylogenetic trees

grass (7.2.0-2)

Geographic Resources Analysis Support System (GRASS GIS)

grass-core (7.2.0-2)

GRASS GIS core components

grass-gui (7.2.0-2)

GRASS GIS graphical user interfaces

gravit (0.5.1+dfsg-2+b2)

visually stunning gravity simulator

gravit-data (0.5.1+dfsg-2)

data files for Gravit

gri (2.12.23-10)

a language for scientific illustration

grinder (0.5.4-1)

Versatile omics shotgun and amplicon sequencing read simulator

gromacs (2016.1-2)

Molecular dynamics simulator, with building and analysis tools

gromacs-data (2016.1-2)

GROMACS molecular dynamics sim, data and documentation

gromacs-mpich (2016.1-2)

Molecular dynamics sim, binaries for MPICH parallelization

gromacs-openmpi (2016.1-2)

Molecular dynamics sim, binaries for OpenMPI parallelization

gubbins (2.2.0-1)

phylogenetic analysis of genome sequences

gvb (1.4-1)

visual simulator of 1 and 2-dimensional vibrations

gwama (2.2.2+dfsg-1)

Genome-Wide Association Meta Analysis

gwyddion (2.47-1)

Scanning Probe Microscopy visualization and analysis tool

gwyddion-common (2.47-1)

architecture-independent files for Gwyddion SPM analysis tool

gwyddion-plugins (2.47-1)

plugins for Gwyddion SPM analysis tool

gyoto (1.2.0-2)

General relativistic geodesic integration and ray-tracing

gyoto-bin (1.2.0-2)

General relativistic ray-tracing command-line interface

h5utils (1.12.1-6+b1)

HDF5 files visualization tools

harminv (1.4-1+b2)

extraction of complex frequencies and amplitudes from time series

harvest-tools (1.3-1)

archiving and postprocessing for reference-compressed genomic multi-alignments

hdf-compass (0.6.0-1)

viewer for HDF5 and related formats

hdf5-helpers (1.10.0-patch1+docs-3+deb9u1)

Hierarchical Data Format 5 (HDF5) - Helper tools

hdf5-tools (1.10.0-patch1+docs-3+deb9u1)

Hierarchical Data Format 5 (HDF5) - Runtime tools

herisvm (0.7.0-1)

machine learning tools for classification algorithms

hfst (3.10.0~r2798-3)

Helsinki Finite-State Transducer Technology

hfst-ospell (0.4.0~r4643-4+b2)

Spell checker library and tool based on HFST

hhsuite (3.0~beta2+dfsg-3)

sensitive protein sequence searching based on HMM-HMM alignment

hhsuite-data (3.0~beta2+dfsg-3)

sensitive protein sequence searching based on HMM-HMM alignment (data)

hilive (0.3-2)

realtime alignment of Illumina reads

hisat2 (2.0.5-1)

graph-based alignment of short nucleotide reads to many genomes

hmmer (3.1b2+dfsg-5)

profile hidden Markov models for protein sequence analysis

hmmer2 (2.3.2-13)

profile hidden Markov models for protein sequence analysis

hmmer2-pvm (2.3.2-13)

HMMER programs with PVM (Parallel Virtual Machine) support

hodie (1.5-2+b1)

prints the date in latin

horae (071~svn537-2.1) [contrib]

interactive graphical processing and analysis of EXAFS data

hpcc (1.4.3-1+b5)

HPC Challenge benchmark

htcondor (8.4.11~dfsg.1-1)

distributed workload management system

hyphy-common (2.2.7+dfsg-1)

Hypothesis testing using Phylogenies (common files)

hyphy-mpi (2.2.7+dfsg-1+b2)

Hypothesis testing using Phylogenies (MPI version)

hyphy-pt (2.2.7+dfsg-1+b2)

Hypothesis testing using Phylogenies (pthreads version)

hyphygui (2.2.7+dfsg-1+b2)

Hypothesis testing using Phylogenies (GTK+ gui)

idba (1.1.3-1)

iterative De Bruijn Graph De Novo short read assembler for transcriptome

ifeffit (2:1.2.11d-10.1) [contrib]

Interactive XAFS analysis program

ifrit (4.1.2-5+b5)

powerful tool for visualizing 3-dimensional data sets

igv (2.3.90+dfsg-1) [non-free]

Integrative Genomics Viewer

imagej (1.51i+dfsg-2)

Image processing program inspired by NIH Image

imagevis3d (3.1.0-5)

desktop volume rendering application for large data

imview (1.1.9c-17+b1)

Image viewing and analysis application

indelible (1.03-2+b1)

powerful and flexible simulator of biological evolution

indigo-utils (1.1.12-2)

Organic Chemistry Toolkit Utilities

infernal (1.1.2-1)

inference of RNA secondary structural alignments

ipig (0.0.r5-2)

integrating PSMs into genome browser visualisations

iqtree (1.5.3+dfsg-2)

efficient phylogenetic software by maximum likelihood

irstlm (6.00.05-2)

IRST Language Modeling Toolkit

ismrmrd-schema (1.3.3-1)

schema for ISMRMRD

ismrmrd-tools (1.3.3-1+b1)

command-line tools for ISMRMRD

itksnap (3.4.0-2+b3)

semi-automatic segmentation of structures in 3D images

iva (1.0.8+ds-1)

iterative virus sequence assembler

jaligner (1.0+dfsg-4)

Smith-Waterman algorithm with Gotoh's improvement

jblas (1.2.3-6)

fast linear algebra library for Java

jellyfish (2.2.6-1+b1)

count k-mers in DNA sequences

jellyfish-examples (2.2.6-1+b1)

count k-mers in DNA sequences (examples for testing)

jemboss (6.6.0+dfsg-6)

graphical user interface to EMBOSS

jmodeltest (2.1.10+dfsg-5)

HPC selection of models of nucleotide substitution

jmol (14.6.4+2016.11.05+dfsg1-3)

Molecular Viewer

jsamp (1.3.5-1)

Java Simple Application Messaging Protocol tool for VO

julia (0.4.7-6+b3)

high-performance programming language for technical computing

julia-common (0.4.7-6)

high-performance programming language for technical computing (common files)

jupyter-notebook (4.2.3-4)

Jupyter interactive notebook

kalign (1:2.03+20110620-3)

Global and progressive multiple sequence alignment

kalzium (4:16.08.3-1)

periodic table and chemistry tools

kalzium-data (4:16.08.3-1)

data files for Kalzium

khmer (2.0+dfsg-10)

in-memory DNA sequence kmer counting, filtering & graph traversal

khmer-common (2.0+dfsg-10)

common files for the khmer project tools

kineticstools (0.6.1+20161222-1)

detection of DNA modifications

kineticstools-data (0.6.1+20161222-1)

detection of DNA modifications -- data files

king-probe (2.13.110909-2)

Evaluate and visualize protein interatomic packing

kissplice (2.4.0-p1-1)

Detection of various kinds of polymorphisms in RNA-seq data

klustakwik (2.0.1-1+b2)

automatic sorting of the samples (spikes) into clusters

kmc (2.3+dfsg-5)

count kmers in genomic sequences

kmer (0~20150903+r2013-3)

suite of tools for DNA sequence analysis

konclude (0.6.2~dfsg-3+b1)

tableau-based description logic reasoner for the semantic web

kraken (0.10.5~beta-2+b1)

assigning taxonomic labels to short DNA sequences

kst (2.0.3-5+b4 [mips], 2.0.3-5+b3 [amd64, arm64, armel, armhf, i386, mips64el, mipsel, ppc64el, s390x])

scientific data plotting tool

kst-data (2.0.3-5)

set of data files for kst

kstars (4:16.08.3-2)

desktop planetarium for KDE

kstars-data (4:16.08.3-2)

data files for KStars desktop planetarium

kstars-data-extra-tycho2 (1.1r1-9.1) [non-free]

Tycho-2 star catalog for KStars

kxterm (20061220+dfsg3-4.3)

CERNLIB data analysis suite - KUIP terminal emulator

lambda-align (1.0.1-2)

Local Aligner for Massive Biological DatA

lammps (0~20161109.git9806da6-7)

Molecular Dynamics Simulator

last-align (830-1)

genome-scale comparison of biological sequences

lbt (1.2.2-6)

converts from LTL formulas to Büchi automata

leaff (0~20150903+r2013-3)

biological sequence library utilities and applications

lefse (1.0+20160802-1)

determine features of organisms, clades, taxonomic units, genes

lhapdf-pdfsets-minimal (5.9.1-5)

Minimal PDF Sets of LHAPDF

libadios-bin (1.11.0-1+b1)

ADIOS Adaptable IO system for simulations - binaries

libapertium3-3.4-0 (3.4.0~r61013-5+b1)

Shared library for Apertium

libball1.4-data (1.4.3~beta1-3)

Biochemical Algorithms Library (data files)

libcamitk4 (4.0.4-2)

Computer Assisted Medical Intervention Tool Kit - runtime

libcassie1v5 (1.0.5-1+b1 [amd64], 1.0.5-1 [arm64, armel, armhf, i386, mips, mips64el, mipsel, ppc64el, s390x])

library implementating search algorithms

libcg3-0 (0.9.9~r11624-1+b3)

Runtime for CG-3

libclhep2.1v5 (2.1.4.1+dfsg-1)

CLHEP: A Class Library for High Energy Physics

libdivsufsort3 (2.0.1-2)

fast suffix array construction

libdynamicedt3d1.8 (1.8.1+dfsg-1)

Incrementally updatable Euclidean distance transform library

libeccodes-data (2.0.2-5)

GRIB and BUFR enecoding/encoding software library - data

libgeotiff-epsg (1.4.2-1) [non-free]

GeoTIFF library -- EPSG Geodetic Parameter Dataset

libgfsgl0 (20121130+dfsg-4)

graphical viewer for Gerris simulation files. Shared library

libghemical-data (3.0.0-4.1)

Molecular Modelling Library (data files)

libgnuradio-fcdproplus3.7.10 (3.7.25.4b6464b-2+b2)

Funcube Dongle Pro Plus controller for GNU Radio (runtime)

libgrits5 (0.8.1-2)

Grits is a Virtual Globe library

libgtkdatabox-0.9.3-0-glade (1:0.9.3.0+dfsg-3)

Gtk+ library to display large amounts of numerical data (glade API)

libgtkdatabox-0.9.3-0-libglade (1:0.9.3.0+dfsg-3)

Gtk+ library to display large amounts of numerical data (glade lib)

libgyoto6 (1.2.0-2)

Gyoto framework main library an standard plug-in

libhdf5-jni (1.10.0-patch1+docs-3+deb9u1)

native library used by libhdf5-java

libhfst45 (3.10.0~r2798-3)

Helsinki Finite-State Transducer Technology Libraries

libhfstospell5 (0.4.0~r4643-4+b2)

HFST spell checker runtime libraries

libismrmrd1.3 (1.3.3-1+b1)

ISMRM Raw Data format (ISMRMRD)

liblas-bin (1.8.1-3+b1)

ASPRS LiDAR data translation toolset

liblemon-utils (1.3.1+dfsg-1+b2)

Library for Efficient Modeling and Optimization in Networks (utilities)

libliggghts3 (3.5.0+repack1-10)

Open Source DEM Particle Simulation Software. Shared library

liblinear-tools (2.1.0+dfsg-2)

Standalone applications for LIBLINEAR

liblorene-debian1 (0.0.0~cvs20161116+dfsg-1)

liblorene shared library

liblorene-export-debian0 (0.0.0~cvs20161116+dfsg-1)

liblorene_export shared library

liblorenef77-debian1 (0.0.0~cvs20161116+dfsg-1)

liblorenef77 shared library

liblttoolbox3-3.3-0v5 (3.3.3~r68466-2+b1)

Shared library for lttoolbox

libncarg-bin (6.3.0-13)

NCAR command-language library - development tools

libncarg-data (6.3.0-13)

NCAR command-language library - Data

libngram-tools (1.3.0-1)

OpenGRM n-gram Language Modeling toolkit

libocas-tools (0.97+dfsg-3)

Standalone applications implementing the OCAS solver

liboctomap1.8 (1.8.1+dfsg-1)

3D occupancy grid mapping approach library for mapping

liboctovis1.8 (1.8.1+dfsg-1)

Visualization library for OctoMap

libopenfoam (4.1+dfsg1-1)

Set of programs for Computational Fluid Dynamics (CFD). Libraries

libopengm-bin (2.3.6+20160905-1+b2)

command line tools for OpenGM

libotb (5.8.0+dfsg-3)

ORFEO Toolbox library metapackage

libotb-apps (5.8.0+dfsg-3)

Plugins for ORFEO Toolbox applications

libpwiz-tools (3.0.9393-1+b2)

ProteoWizard command line tools

libqgis-customwidgets (2.14.11+dfsg-3+deb9u1)

QGIS custom widgets for Qt Designer

libqgis-server2.14.11 (2.14.11+dfsg-3+deb9u1)

QGIS - shared server library

libqtpropertybrowser4 (4.0.4-2)

Qt Property Browser Library - runtime

librasterlite2-1 (1.0.0~rc0+devel1-4)

library for huge raster coverages using a SpatiaLite DBMS

libsilo-bin (4.10.2-6+b3)

Utilities to manipulate libsilo files

libsimgrid3.14 (3.14.159-2)

Toolkit for scalable simulation of distributed applications

libstxxl1v5 (1.4.1-2+b1)

C++ Standard Template Library for extra large datasets

libvcflib-tools (1.0.0~rc1+dfsg1-3)

C++ library for parsing and manipulating VCF files (tools)

libxy-bin (1.3-1.1+b1)

xylib - utilities

libyade (2017.01a-8)

Platform for discrete element modeling. Libraries

liggghts (3.5.0+repack1-10)

Open Source DEM Particle Simulation Software.

litl-tools (0.1.8-2+b2)

Lightweight Trace Library - tools

logcentral (2.7-1.1+b1)

Logging service for distributed applications

logcentral-tools (2.7-1.1+b1)

Logging service for distributed applications

logol (1.7.5-1)

Pattern matching tool using Logol language

logol-bin (1.7.5-1)

Pattern matching tool using Logol language

loki (2.4.7.4-6+b1)

MCMC linkage analysis on general pedigrees

looptools (2.8-1+b1)

Integral Evaluator of One-loop Feynman Diagram

lorene (0.0.0~cvs20161116+dfsg-1)

framework for numerical relativity

lorene-codes-src (0.0.0~cvs20161116+dfsg-1)

source files of LORENE-based codes

ltrsift (1.0.2-7)

postprocessing and classification of LTR retrotransposons

ltrsift-examples (1.0.2-7)

example data for LTRsift

lttoolbox-dev (3.3.3~r68466-2+b1)

Development tools and library for lttoolbox

lutefisk (1.0.7+dfsg-4+b1)

de novo interpretation of peptide CID spectra

macs (2.1.1.20160309-1)

Model-based Analysis of ChIP-Seq on short reads sequencers

macsyfinder (1.0.2-3)

detection of macromolecular systems in protein datasets

maffilter (1.1.0-1+dfsg-2+b2)

process genome alignment in the Multiple Alignment Format

maffilter-examples (1.1.0-1+dfsg-2)

process genome alignment in the Multiple Alignment Format (example data)

mafft (7.307-1)

Multiple alignment program for amino acid or nucleotide sequences

mapdamage (2.0.6+dfsg-2)

tracking and quantifying damage patterns in ancient DNA sequences

mapsembler2 (2.2.3+dfsg-3+b1)

bioinformatics targeted assembly software

maq (0.7.1-7)

maps short fixed-length polymorphic DNA sequence reads to reference sequences

maqview (0.2.5-7+b1)

graphical read alignment viewer for short gene sequences

mash (1.1.1-2)

fast genome and metagenome distance estimation using MinHash

massxpert (3.6.1-1)

linear polymer mass spectrometry software

massxpert-data (3.6.1-1)

linear polymer mass spectrometry software - arch-indep data

matlab-gdf (0.1.2-2) [contrib]

IO library for the GDF -- Matlab interface

maude (2.7-2+b1)

high-performance logical framework

mauve-aligner (2.4.0+4734-3)

multiple genome alignment

mayavi2 (4.5.0-1)

scientific visualization package for 2-D and 3-D data

mbt (3.2.16-1+b1)

memory-based tagger-generator and tagger

mbtserver (0.11-1+b1)

Server extensions for the MBT tagger

meep (1.3-4+b1)

software package for FDTD simulation

meep-lam4 (1.3-2+b1)

software package for FDTD simulation, parallel (OpenMPI) version

meep-mpi-default (1.3-3+b4 [s390x], 1.3-3+b3 [amd64, arm64, armel, armhf, i386, mips, mips64el, mipsel, ppc64el])

software package for FDTD simulation, parallel (OpenMPI) version

meep-mpich2 (1.3-4+b1)

software package for FDTD simulation, parallel (OpenMPI) version

meep-openmpi (1.3-3+b3 [amd64, arm64, armel, armhf, i386, mips, mips64el, mipsel, ppc64el], 1.3-3+b2 [s390x])

software package for FDTD simulation, parallel (OpenMPI) version

melting (4.3.1+dfsg-2+b1)

compute the melting temperature of nucleic acid duplex

melting-gui (4.3.1+dfsg-2)

graphical interface to compute the melting temperature of nucleic acid duplex

merkaartor (0.18.3+ds-1+b1)

map editor for OpenStreetMap.org

meryl (0~20150903+r2013-3)

in- and out-of-core kmer counting and utilities

metaphlan2 (2.6.0+ds-2)

Metagenomic Phylogenetic Analysis

metaphlan2-data (2.6.0+ds-2)

data package for Metagenomic Phylogenetic Analysis

metastudent (2.0.1-4)

predictor of Gene Ontology terms from protein sequence

metastudent-data (2.0.1-2)

predictor of Gene Ontology terms from protein sequence - data files

metastudent-data-2 (1.0.0-2)

predictor of Gene Ontology terms from protein sequence - data #2

metview (4.8.0-4)

Interactive data visualization and analysis environment,

metview-data (4.8.0-4)

Data needed for the Metview data analysis environment

mgltools-bhtree (1.5.7-1) [non-free]

Bhtree library extension module

mgltools-cadd (1.5.7-1) [non-free]

Computer Aided Drug Discovery (CADD) Pipeline

mgltools-cmolkit (1.5.7~rc1+cvs.20140424-1) [non-free]

Python classes to interpret trajectories of Gromacs

mgltools-dejavu (1.5.7-1) [non-free]

visualization of 3D geometry using the OpenGL with Python

mgltools-geomutils (1.5.7-1) [non-free]

Python library for geometric analyses

mgltools-mglutil (1.5.7-2) [non-free]

Molecular Graphics Laboratory utility collection

mgltools-molkit (1.5.7~rc1+cvs.20140424-1) [non-free]

Python classes to read and manipulate molecules

mgltools-networkeditor (1.5.7-1) [non-free]

Python GUI library for the editing of networks

mgltools-opengltk (1.5.7-1) [non-free]

Opengltk Python extension

mgltools-pyautodock (1.5.7-1) [non-free]

Python implementation of autodock

mgltools-pybabel (1.5.7-1) [non-free]

molecular structure file access and interpretation

mgltools-pyglf (1.5.7-1) [non-free]

GLF library Python extension to write text in OpenGL

mgltools-scenario2 (1.5.7-1) [non-free]

Python-based viewer of molecular structures

mgltools-sff (1.5.6~rc3~cvs.20120206-1) [non-free]

Simple Force Field for Python

mgltools-support (1.5.7-1) [non-free]

Update mechanism of MGLTools

mgltools-symserv (1.5.7-1) [non-free]

Symetry server

mgltools-utpackages (1.5.7-1) [non-free]

UT Austin software Python extensions

mgltools-viewerframework (1.5.7-1) [non-free]

ViewerFramework supports building visualization applications

mgltools-vision (1.5.7-1) [non-free]

Python-based Visual Programming Environment

mgltools-visionlibraries (1.5.7-1) [non-free]

Extensions for Python-based Visual Programming Environment

mgltools-volume (1.5.7-1) [non-free]

Volume rendering Python package

mgltools-webservices (1.5.7-1) [non-free]

webservices for components of autodocktools

mhap (2.1.1+dfsg-1)

locality-sensitive hashing to detect long-read overlaps

mia-doctools (2.4.3-5)

Helper scripts for run-time document creation

mia-tools (2.4.3-5)

Command line tools for gray scale image processing

mia-viewit (1.0.4-1+b1)

Viewer program for 3D data sets created by using MIA

mialmpick (0.2.13-1)

Tools for landmark picking in 3D volume data sets

microbegps (1.0.0-2)

explorative taxonomic profiling tool for metagenomic data

microbiomeutil (20101212+dfsg1-1)

Microbiome Analysis Utilities

microbiomeutil-data (20101212+dfsg1-1)

Reference 16S sequences and NAST-alignments used by microbiomeutil tools

microhope (4.2.1+dfsg-1)

hardware & software framework to learn microcontrollers

minc-tools (2.3.00+dfsg-1.1+b1)

MNI medical image format tools

minia (1.6906-1+b2)

short-read biological sequence assembler

miniasm (0.2+dfsg-2+b1)

ultrafast de novo assembler for long noisy DNA sequencing reads

minimap (0.2-3+b1)

tool for approximate mapping of long biosequences such as DNA reads

minisat (1:2.2.1-5+b3)

Fast and lightweight SAT solver

minisat+ (1.0-3)

solver for pseudo-Boolean constraints

minisat2 (1:2.2.1-5+b3)

Transitional package for minisat

minisat2

virtual package provided by minisat

mipe (1.1-5)

Tools to store PCR-derived data

mira-assembler (4.9.6-2)

Whole Genome Shotgun and EST Sequence Assembler

mira-rfam-12s-rrna (4.9.6-2)

extract of RFAM 12 rRNA database

missfits (2.8.0-1+b1)

Basic maintenance and packaging tasks on FITS files

mlpack-bin (2.1.1-1)

intuitive, fast, scalable C++ machine learning library (binaries)

mlv-smile (1.47-4+b1)

Find statistically significant patterns in sequences

mmass (5.5.0-5)

Mass spectrometry tool for proteomics

mmass-modules (5.5.0-5)

Mass spectrometry tool for proteomics - extension modules

mobyle (1.5.5+dfsg-2)

Web portal that provides web forms for command-line software

mobyle-programs (5.1.2-1)

Program descriptions for the mobyle portal

mobyle-tutorials (1.5.0-2)

program tutorials for the mobyle portal

mobyle-utils (1.5.5+dfsg-2)

binary tools used by Mobyle

mocassin (2.02.72-2)

MOnte CArlo SimulationS of Ionised Nebulae

mocassin-benchmarks (2.02.72-2)

benchmarks for the photoionisation code MOCASSIN

mocassin-data (2.02.72-2)

atomic and optical data for the photoionisation code MOCASSIN

mocassin-examples (2.02.72-2)

Examples for the photoionisation code MOCASSIN

molds (0.3.1-1+b5 [amd64, arm64, armhf, i386], 0.3.1-1+b4 [ppc64el], 0.3.1-1 [mips64el])

Semi-empirical electronic structure and molecular dynamics

mona (1.4-17-1+b1)

theorem prover based on automata

montage (4.0+dfsg-3+b3)

Toolkit for assembling FITS images into mosaics

montage-gridtools (4.0+dfsg-3+b3)

Create files to run montage on the grid

montecarlo-base (20061220+dfsg3-3.1)

[Physics] Common files for CERNLIB Monte Carlo libraries

montecarlo-data (20061220+dfsg3-3.1)

[Physics] data for CERNLIB Monte Carlo libraries

mopac7-bin (1.15-6+b1)

Semi-empirical Quantum Chemistry Library (binaries)

morse-simulator (1.4-2)

Multi-OpenRobot Simulation Engine

morse-simulator-data (1.4-2)

Multi-OpenRobot Simulation Engine

mothur (1.38.1.1-1)

sequence analysis suite for research on microbiota

mothur-mpi (1.38.1.1-1)

mpi-enabled binary for mothur

mpb (1.5-2+b7 [s390x], 1.5-2+b5 [amd64, armel, armhf, i386, mips, mipsel], 1.5-2+b4 [arm64, ppc64el], 1.5-2+b3 [mips64el])

MIT Photonic-Bands

mpb-mpi (1.5-2+b7 [s390x], 1.5-2+b5 [amd64, armel, armhf, i386, mips, mipsel], 1.5-2+b4 [arm64, ppc64el], 1.5-2+b3 [mips64el])

MIT Photonic-Bands, parallel (mpich) version

mpb-scm (1.5-2)

MIT Photonic-Bands initialisation files

mpqc (2.3.1-18+deb9u1)

Massively Parallel Quantum Chemistry Program

mpqc-openmpi (2.3.1-18+deb9u1)

Massively Parallel Quantum Chemistry Program (OpenMPI transitional package)

mpqc-support (2.3.1-18+deb9u1)

Massively Parallel Quantum Chemistry Program (support tools)

mpqc3 (0.0~git20170114-4)

Massively Parallel Quantum Chemistry Program

mpqc3-data (0.0~git20170114-4)

Massively Parallel Quantum Chemistry Program (data files)

mrbayes (3.2.6+dfsg-1+b4)

Bayesian Inference of Phylogeny

mrbayes-mpi (3.2.6+dfsg-1+b4)

Bayesian Inference of Phylogeny - mpi version

mriconvert (1:2.1.0-1)

medical image file conversion utility

mricron (0.20140804.1~dfsg.1-2+b1)

magnetic resonance image conversion, viewing and analysis

mricron-data (0.20140804.1~dfsg.1-2)

data files for MRIcron

mrpt-apps (1:1.4.0-7+b1 [mips, mips64el, mipsel], 1:1.4.0-7 [amd64, arm64, armel, armhf, i386, ppc64el, s390x])

Mobile Robot Programming Toolkit - Console and GUI applications

mrpt-common (1:1.4.0-7)

Mobile Robot Programming Toolkit - Example datasets and files

mrs (6.0.5+dfsg-2+b2)

Information Retrieval System for Biomedical databanks

mssstest (3.0-5) [non-free]

Normalisation of disease scores for patients with Multiple Sclerosis

mummer (3.23+dfsg-2)

Efficient sequence alignment of full genomes

munipack (0.5.7-2)

Astronomical photometry software package

munipack-cli (0.5.7-2)

Command line interface of Munipack

munipack-core (0.5.7-2)

Core routines of Munipack

munipack-gui (0.5.7-2)

Graphical user interface of Munipack

murasaki (1.68.6-6+b4)

homology detection tool across multiple large genomes

murasaki-common (1.68.6-6)

homology detection tool across multiple large genomes (common files)

murasaki-mpi (1.68.6-6+b4)

homology detection tool across multiple large genomes (MPI-version)

muscle (1:3.8.31+dfsg-2)

Multiple alignment program of protein sequences

music-bin (1.0.7-1.3)

Multi-Simulation Coordinator for MPI -- Utilities

mustang (3.2.3-1)

multiple structural alignment of proteins

mustang-testdata (3.2.3-1)

multiple structural alignment of proteins, test data

nanopolish (0.5.0-1+b1)

consensus caller for nanopore sequencing data

nast-ier (20101212+dfsg1-1+b1)

NAST-based DNA alignment tool

nastran (0.1.95-1) [non-free]

NASA Structural Analysis System

ncbi-blast+ (2.6.0-1)

next generation suite of BLAST sequence search tools

ncbi-blast+-legacy (2.6.0-1)

NCBI Blast legacy call script

ncbi-entrez-direct (6.10.20170123+ds-1)

NCBI Entrez utilities on the command line

ncbi-epcr (2.3.12-1-4)

Tool to test a DNA sequence for the presence of sequence tagged sites

ncbi-rrna-data (6.1.20170106-2)

large rRNA BLAST databases distributed with the NCBI toolkit

ncbi-seg (0.0.20000620-3+b1)

tool to mask segments of low compositional complexity in amino acid sequences

ncbi-tools-bin (6.1.20170106-2)

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11 (6.1.20170106-2)

NCBI libraries for biology applications (X-based utilities)

ncl-ncarg (6.3.0-13)

NCAR Command Language and NCAR graphics

ncl-tools (2.1.18+dfsg-2+b1)

tools to deal with NEXUS files

nco (4.6.3-1+b1)

Command-line operators to analyze netCDF files

ncoils (2002-4+b1)

coiled coil secondary structure prediction

ncview (2.1.7+ds-1+b2)

X11 visual browser for NetCDF format files

neat (2.0-2)

Nebular Empirical Analysis Tool

neobio (0.0.20030929-2)

computes alignments of amino acid and nucleotide sequences

netcdf-bin (1:4.4.1.1-2)

Programs for reading and writing NetCDF files

neurodebian (0.37.6)

neuroscience-oriented distribution - repository configuration

neurodebian-archive-keyring (0.37.6)

neuroscience-oriented distribution - GnuPG archive keys

neurodebian-desktop (0.37.6)

neuroscience-oriented distribution - desktop integration

neurodebian-dev (0.37.6)

neuroscience-oriented distribution - development tools

neurodebian-popularity-contest (0.37.6)

neuroscience-oriented distribution - popcon integration

nifti2dicom (0.4.11-1+b3)

convert 3D medical images to DICOM 2D series

nifti2dicom-data (0.4.11-1)

data files for nifti2dicom

njplot (2.4-7)

phylogenetic tree drawing program

norsnet (1.0.17-2)

tool to identify unstructured loops in proteins

norsp (1.0.6-2)

predictor of non-regular secondary structure

numdiff (5.8.1-2+b1)

Compare similar files with numeric fields

nutsqlite (1.9.9.3-2)

Dietary nutrition analysis software

oar-common (2.5.7-3)

OAR batch scheduler common package

oar-node (2.5.7-3)

OAR batch scheduler node package

oar-server (2.5.7-3)

OAR batch scheduler server package

oar-server-mysql (2.5.7-3)

OAR batch scheduler MySQL server backend package

oar-server-pgsql (2.5.7-3)

OAR batch scheduler PostgreSQL server backend package

oar-user (2.5.7-3)

OAR batch scheduler user package

oar-user-mysql (2.5.7-3)

OAR batch scheduler MySQL user backend package

oar-user-pgsql (2.5.7-3)

OAR batch scheduler PostgreSQL user backend package

oar-web-status (2.5.7-3)

OAR batch scheduler visualization tool package

obdgpslogger (0.16-1.3+b1)

suite of tools to log OBDII and GPS data

oce-draw (0.17.2-2)

OpenCASCADE Community Edition CAE platform shared library

octave-bart (0.4.00-1)

Octave bindings for BART

octave-biosig (1.3.0-2.2)

Octave bindings for BioSig library

octave-gdf (0.1.2-2+b8 [mips], 0.1.2-2+b7 [amd64, armel, armhf, i386, mipsel, s390x], 0.1.2-2+b5 [ppc64el], 0.1.2-2+b4 [arm64], 0.1.2-2+b2 [mips64el])

IO library for the GDF -- Octave interface

octave-lhapdf (5.9.1-5)

Octave Bindings for LHAPDF

octave-psychtoolbox-3 (3.0.14.20170103+git6-g605ff5c.dfsg1-1)

toolbox for vision research -- Octave bindings

octomap-tools (1.8.1+dfsg-1)

Tools for 3D occupancy grid mapping

octovis (1.8.1+dfsg-1)

Visualization tool for OctoMap

odil (0.7.3-1)

C++11 library for the DICOM standard (application)

ogdi-bin (3.2.0+ds-2)

Open Geographic Datastore Interface Library -- utilities

openbabel (2.3.2+dfsg-3)

Chemical toolbox utilities (cli)

openbabel-gui (2.3.2+dfsg-3)

Chemical toolbox utilities (graphical user interface)

opencaster (3.2.2+dfsg-1.1+b1)

MPEG2 transport stream data generator and packet manipulator

openfoam (4.1+dfsg1-1)

Set of programs for Computational Fluid Dynamics (CFD). Binaries

openfoam-examples (4.1+dfsg1-1)

Set of programs for Computational Fluid Dynamics (CFD). Examples

openmolar (1.0.15-gd81f9e5-1)

dental practice management software

openmx (3.7.6-1+b6)

package for nano-scale material simulations

openmx-data (3.7.6-1)

package for nano-scale material simulations (data)

openrocket (15.03)

Model Rocket Simulator

opensesame (0.27.4-2.1)

graphical experiment builder for the social sciences

openturns-examples (1.7-3)

examples of OpenTURNS functionalities

openturns-validation (1.7-3)

validation files for OpenTURNS

openuniverse (1.0beta3.1+dfsg-6)

3D Universe Simulator

openuniverse-common (1.0beta3.1+dfsg-6)

3D Universe Simulator data files

optgeo (2.23-1+b1)

simulator for geometrical optics

opticalraytracer (3.2-1.1)

Virtual lens design workshop

origami (1.2.7+really0.7.4-1.1)

command-line management tool for Folding @ Home clients

orthanc (1.2.0+dfsg-1)

Lightweight, RESTful DICOM server for medical imaging

orthanc-dicomweb (0.3+dfsg-1+b2)

Plugin to extend Orthanc with support of WADO and DICOMweb

orthanc-imagej (1.1+dfsg-1)

ImageJ plugin to import images from Orthanc

orthanc-postgresql (2.0-3+b1)

Plugins to use PostgreSQL as a database back-end to Orthanc

orthanc-webviewer (2.2-1+b2)

Web viewer of medical images for Orthanc

ossim-core (1.8.20.3+ds-5+b1)

OSSIM core utilities

otb-bin (5.8.0+dfsg-3)

ORFEO Toolbox command line applications

otb-bin-qt (5.8.0+dfsg-3)

ORFEO Toolbox graphical user interface applications

otb-testdriver (5.8.0+dfsg-3)

ORFEO Toolbox library - OTBTestDriver

otf-trace (1.12.5+dfsg-2+b2)

Open Trace Format support library - development files

ovito (2.8.1+dfsg2-5)

visualization and analysis tool for atomistic simulation data

p4vasp (0.3.29+dfsg-3)

visualization suite for the Vienna Ab-initio Simulation Package (VASP)

paje.app (1.98-1+b4)

generic visualization tool (Gantt chart and more)

paml (4.8+dfsg-1) [non-free]

Phylogenetic Analysis by Maximum Likelihood (PAML)

paraclu (9-1+b2)

Parametric clustering of genomic and transcriptomic features

parafly (0.0.2013.01.21-3+b1)

parallel command processing using OpenMP

paraview (5.1.2+dfsg1-2)

Parallel Visualization Application

parsinsert (1.04-2)

Parsimonious Insertion of unclassified sequences into phylogenetic trees

parsnp (1.2+dfsg-3)

rapid core genome multi-alignment

paw (1:2.14.04.dfsg.2-9.1)

Physics Analysis Workstation - a graphical analysis program

paw++ (1:2.14.04.dfsg.2-9.1)

Physics Analysis Workstation (Lesstif-enhanced version)

paw-common (1:2.14.04.dfsg.2-9.1)

Physics Analysis Workstation (common files)

paw-demos (1:2.14.04.dfsg.2-9.1)

Physics Analysis Workstation examples and tests

pbbamtools (0.7.4+ds-1)

processing Pacific Biosciences binary alignment/map files

pbbarcode (0.8.0-4)

annotate PacBio sequencing reads with barcode information

pbdagcon (0.3+20161121+ds-1)

sequence consensus using directed acyclic graphs

pbgenomicconsensus (2.1.0-1)

Pacific Biosciences variant and consensus caller

pbh5tools (0.8.0+dfsg-5)

tools for manipulating Pacific Biosciences HDF5 files

pbhoney (15.8.24+dfsg-2)

genomic structural variation discovery

pbjelly (15.8.24+dfsg-2)

genome assembly upgrading tool

pbsim (1.0.3-2)

simulator for PacBio sequencing reads

pdb2pqr (2.1.1+dfsg-2)

Preparation of protein structures for electrostatics calculations

pegasus-wms (4.4.0+dfsg-6)

Scientific workflow management system for HTCondor

perlprimer (1.2.3-1)

Graphical design of primers for PCR

perm (0.4.0-2)

efficient mapping of short reads with periodic spaced seeds

phipack (0.0.20160614-2)

PHI test and other tests of recombination

phybin (0.3-1+b1)

binning/clustering newick trees by topology

phylip (1:3.696+dfsg-5)

package of programs for inferring phylogenies

phyml (3:3.2.0+dfsg-7+b1)

Phylogenetic estimation using Maximum Likelihood

physamp (0.2.0-1+b1)

sample sequence alignment according to its corresponding phylogenetic tree

phyutility (2.7.3-1)

simple analyses or modifications on both phylogenetic trees and data matrices

picard-tools (2.8.1+dfsg-1)

Command line tools to manipulate SAM and BAM files

picosat (960-1+b2)

SAT solver with proof and core support

piler (0~20140707-1+b1)

genomic repeat analysis

pirs (2.0.2+dfsg-5.1+b1)

Profile based Illumina pair-end Reads Simulator

pirs-examples (2.0.2+dfsg-5.1)

profile basd Illumina pair-end Reads Simulator (example data)

pirs-profiles (2.0.2+dfsg-5.1)

profile basd Illumina pair-end Reads Simulator (profile data)

pktools (2.6.7-3)

GDAL add-on tools to perform useful raster processing

placnet (1.03-2)

Plasmid Constellation Network project

planets (0.1.13-16)

Gravitation simulation of planetary bodies

plast (2.3.1+dfsg-4)

Parallel Local Sequence Alignment Search Tool

plast-example (2.3.1+dfsg-4)

Parallel Local Sequence Alignment Search Tool (example data)

plastimatch (1.6.5+dfsg.1-1)

medical image reconstruction and registration

plink (1.07-7)

whole-genome association analysis toolset

plink1.9 (1.90~b3.45-170113-1)

whole-genome association analysis toolset

pnetcdf-bin (1.7.0-1+b2)

Programs for reading and writing parallel NetCDF files

poa (2.0+20060928-4+b1)

Partial Order Alignment for multiple sequence alignment

populations (1.2.33+svn0120106-2.1+b1)

population genetic software

poretools (0.6.0+dfsg-2)

toolkit for nanopore nucleotide sequencing data

poretools-data (0.6.0+dfsg-2)

toolkit for nanopore nucleotide sequencing data -- sample datasets

pp-popularity-contest (1.0.6-2+b4 [amd64, armel, armhf, i386, mips, mipsel, s390x], 1.0.6-2+b3 [arm64, ppc64el], 1.0.6-2+b2 [mips64el])

PredictProtein popularity contest

pprepair (0.0~20160321-87ffae5-1+b3)

planar partition repair tool

praat (6.0.23-1)

program for speech analysis and synthesis

prank (0.0.150803-2)

Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

predictnls (1.0.20-3)

prediction and analysis of protein nuclear localization signals

predictprotein (1.1.07-2)

suite of protein sequence analysis tools

prepair (0.7-6+b4)

polygon repair tool

prepair-data (0.7-6)

polygon repair tool -- example data

prime-phylo (1.0.11-4+b3)

bayesian estimation of gene trees taking the species tree into account

primer3 (2.3.7-3)

tool to design flanking oligo nucleotides for DNA amplification

primer3-examples (2.3.7-3)

tool to design flanking oligo nucleotides for DNA amplification (examples)

proalign (0.603-2)

Probabilistic multiple alignment program

probabel (0.4.5-3+b1)

Toolset for Genome-Wide Association Analysis

probabel-examples (0.4.5-3)

Example files for ProbABEL

probalign (1.4-5)

multiple sequence alignment using partition function posterior probabilities

probcons (1.12-11)

PROBabilistic CONSistency-based multiple sequence alignment

probcons-extra (1.12-11)

Extra programs from the probcons package

proda (1.0-10)

multiple alignment of protein sequences

prodigal (1:2.6.3-1+b1)

Microbial (bacterial and archaeal) gene finding program

profbval (1.0.22-4)

predictor of flexible/rigid protein residues from sequence

profisis (1.0.11-3)

prediction of protein-protein interaction sites from sequence

profnet-bval (1.0.22-4)

neural network architecture for profbval

profnet-chop (1.0.22-4)

neural network architecture for profchop

profnet-con (1.0.22-4)

neural network architecture for profcon

profnet-isis (1.0.22-4)

neural network architecture for profisis

profnet-md (1.0.22-4)

neural network architecture for metadisorder

profnet-norsnet (1.0.22-4)

neural network architecture for norsnet

profnet-prof (1.0.22-4)

neural network architecture for profacc

profnet-snapfun (1.0.22-4)

neural network architecture for snapfun

profphd (1.0.42-1)

secondary structure and solvent accessibility predictor

profphd-net (1.0.22-4)

neural network architecture for profphd

profphd-utils (1.0.10-3+b1)

profphd helper utilities convert_seq and filter_hssp

proftmb (1.1.12-6+b1)

per-residue prediction of bacterial transmembrane beta barrels

progressivemauve (1.2.0+4713-2+b2)

multiple genome alignment algorithms

proj-bin (4.9.3-1)

Cartographic projection library (tools)

proj-rdnap (2008-6) [non-free]

RDNAP grid correction files for PROJ.4

prooftree (0.13-1)

proof-tree visualization for Proof General

proteinortho (5.15+dfsg-1)

Detection of (Co-)orthologs in large-scale protein analysis

prottest (3.4.2+dfsg-2)

selection of best-fit models of protein evolution

psfex (3.17.1+dfsg-3+b2)

Point Spread Function model extractor

psi3 (3.4.0-6+b2 [mips64el], 3.4.0-6+b1 [amd64, arm64, armel, armhf, i386, mips, mipsel, ppc64el, s390x])

Quantum Chemical Program Suite

psi4 (1:1.0-1+b1)

Quantum Chemical Program Suite

psi4-data (1:1.0-1)

Quantum Chemical Program Suite (data files)

psychopy (1.83.04.dfsg-2)

environment for creating psychology stimuli in Python

psychtoolbox-3-common (3.0.14.20170103+git6-g605ff5c.dfsg1-1)

toolbox for vision research -- arch/interpreter independent part

psychtoolbox-3-lib (3.0.14.20170103+git6-g605ff5c.dfsg1-1)

toolbox for vision research -- arch-specific parts

purify (2.0.0-1+b1 [amd64], 2.0.0-1 [armel, armhf, i386])

Collection of routines for radio interferometric imaging

pyfai (0.13.0+dfsg-1)

Fast Azimuthal Integration scripts

pyfr (1.5.0-1)

flux reconstruction in Python

pymca (5.1.3+dfsg-1)

Applications and toolkit for X-ray fluorescence analysis -- scripts

pymca-data (5.1.3+dfsg-1)

Architecture independent data files for PyMca

pymoctool (0.4.2-1)

Python Multi-Order Coverage maps tool for Virtual Observatory

pymol (1.8.4.0+dfsg-1)

Molecular Graphics System

pymol-data (1.8.4.0+dfsg-1)

data files for PyMOL

pysatellites (2.4-2)

simulates the launching of satellites

python-drizzle-testdata (1.3-2)

Dithered image combination for Python (Test data)

python-escript (5.0-3)

Escript/Finley finite elements Python2 system (with OpenMP)

python-escript-doc (5.0-3)

Documentation for Escript/Finley

python-escript-mpi (5.0-3)

Escript/Finley finite elements Python2 system (OpenMP + MPI)

python-expyriment (0.7.0+git34-g55a4e7e-3.2)

Python library for cognitive and neuroscientific experiments

python-pybigwig (0.3.2-1)

Python 2 module for quick access to bigBed and bigWig files

python-pynlpl (1.1.2-1)

PyNLPl is a library for Natural Language Processing (Python 2 version)

python3-escript (5.0-3)

Escript/Finley finite elements Python3 system (with OpenMP)

python3-escript-mpi (5.0-3)

Escript/Finley finite elements Python3 system (OpenMP + MPI)

python3-pybigwig (0.3.2-1)

Python 3 module for quick access to bigBed and bigWig files

python3-pynlpl (1.1.2-1)

PyNLPl is a library for Natural Language Processing (Python 3 version)

pyzo (4.3.1-1+deb9u1)

interactive editor for scientific Python

qfits-tools (6.2.0-8+b2)

FITS manipulation tools

qfitsview (3.3+p1+dfsg-2)

FITS file viewer based on DPUSER

qgis (2.14.11+dfsg-3+deb9u1)

Geographic Information System (GIS)

qgis-api-doc (2.14.11+dfsg-3+deb9u1)

QGIS API documentation

qgis-common (2.14.11+dfsg-3+deb9u1)

QGIS - architecture-independent data

qgis-plugin-grass (2.14.11+dfsg-3+deb9u1)

GRASS plugin for QGIS

qgis-plugin-grass-common (2.14.11+dfsg-3+deb9u1)

GRASS plugin for QGIS - architecture-independent data

qgis-provider-grass (2.14.11+dfsg-3+deb9u1)

GRASS provider for QGIS

qgis-providers (2.14.11+dfsg-3+deb9u1)

collection of data providers to QGIS

qgis-providers-common (2.14.11+dfsg-3+deb9u1)

collection of data providers to QGIS - architecture-independent files

qgis-server (2.14.11+dfsg-3+deb9u1)

QGIS server providing various OGC services

qmapshack (1.7.2-1)

GPS mapping (GeoTiff and vector) and GPSr management

qmc (0.94-3.1)

Quine McClusky Simplification Tool

qnifti2dicom (0.4.11-1+b3)

convert 3D medical images to DICOM 2D series (gui)

qrisk2 (0.1.20150729-2)

cardiovascular disease risk calculator

qthid-fcd-controller (4.1-3+b1)

Funcube Dongle controller

qtltools (1.1+dfsg-1)

Tool set for molecular QTL discovery and analysis

quantum-espresso (6.0-3)

Electronic-Structure and Ab-Initio Molecular Dynamics Suite

quantum-espresso-data (6.0-3)

Electronic-Structure and Ab-Initio Molecular Dynamics Suite (Documentation)

qutemol (0.4.1~cvs20081111-6+b2)

interactive visualization of macromolecules

rambo-k (1.21+dfsg-1)

Read Assignment Method Based On K-mers

rapmap (0.4.0+dfsg-2)

rapid sensitive and accurate DNA read mapping via quasi-mapping

rasmol (2.7.5.2-2)

Visualize biological macromolecules

raster3d (3.0-3-2+b1)

tools for generating images of proteins or other molecules

rate4site (3.0.0-4+b1)

detector of conserved amino-acid sites

rawtran (0.3.8-2+b1)

RAW photo to FITS converter

raxml (8.2.9+dfsg-1+b1)

Randomized Axelerated Maximum Likelihood of phylogenetic trees

ray (2.3.1-4+b1)

de novo genome assemblies of next-gen sequencing data

ray-extra (2.3.1-4)

Scripts and XSL sheets for post-processing for ray

rdkit-data (201603.5-2)

Collection of cheminformatics and machine-learning software (data files)

rdp-classifier (2.10.2-1)

extensible sequence classifier for fungal lsu, bacterial and archaeal 16s

readseq (1-11+b1)

Conversion between sequence formats

reapr (1.0.18+dfsg-3)

universal tool for genome assembly evaluation

relion-bin (1.4+dfsg-2+b2)

toolkit for 3D reconstructions in cryo-electron microscopy

relion-bin+gui (1.4+dfsg-2+b2)

parallel toolkit for 3D reconstructions in cryo-electron microscopy

relion-bin+mpi (1.4+dfsg-2+b2)

parallel toolkit for 3D reconstructions in cryo-electron microscopy

relion-bin+mpi+gui (1.4+dfsg-2+b2)

parallel toolkit for 3D reconstructions in cryo-electron microscopy

repeatmasker-recon (1.08-3+b1)

finds repeat families from biological sequences

reprof (1.0.1-4)

protein secondary structure and accessibility predictor

rna-star (2.5.2b+dfsg-1)

ultrafast universal RNA-seq aligner

rnahybrid (2.1.2-1+b1)

Fast and effective prediction of microRNA/target duplexes

roary (3.8.0+dfsg-1)

high speed stand alone pan genome pipeline

rsem (1.2.31+dfsg-1)

RNA-Seq by Expectation-Maximization

rtax (0.984-5)

Classification of sequence reads of 16S ribosomal RNA gene

ruby-rgfa (1.3.1-1)

parse, edit and write GFA format graphs in Ruby

saga (2.3.1+dfsg-3)

System for Automated Geoscientific Analyses

saga-common (2.3.1+dfsg-3)

SAGA GIS architecture independent files

saint (2.5.0+dfsg-2+b1)

Significance Analysis of INTeractome

salmon (0.7.2+ds1-2+b1)

wicked-fast transcript quantification from RNA-seq data

samtools (1.3.1-3)

processing sequence alignments in SAM and BAM formats

samtools-test (1.3.1-3)

test files for the samtools package

saods9 (7.5+repack1-2)

Image display tool for astronomy

saods9-tclpackages (7.5+repack1-2)

Tcl/Tk packages provided with DS9

sat4j (2.3.5-0.2)

Efficient library of SAT solvers in Java

savi (1.5.0a-1)

satellite constellation visualisation

sbmltoolbox (4.1.0-3)

libsbml toolbox for octave and matlab

scamp (2.0.4-3+b1)

Compute astrometric and photometric solutions

science-astronomy (1.7)

Debian Science Astronomy transitional package

science-astronomy-dev (1.7)

Debian Science Astronomy-dev transitional package

science-biology (1.7)

Debian Science Biology packages

science-chemistry (1.7)

Debian Science Chemistry packages

science-config (1.7)

Debian Science Project config package

science-dataacquisition (1.7)

Debian Science data acquisition packages

science-dataacquisition-dev (1.7)

Debian Science data acquisition development packages

science-distributedcomputing (1.7)

Debian Science Distributed Computing packages

science-economics (1.7)

Debian Science Economics packages

science-electronics (1.7)

Debian Science Electronics packages

science-electrophysiology (1.7)

Debian Science packages for Electrophysiology

science-engineering (1.7)

Debian Science Engineering packages

science-engineering-dev (1.7)

Debian Science Engineering-dev packages

science-financial (1.7)

Debian Science financial engineering and computational finance

science-geography (1.7)

Debian Science Geography packages

science-geometry (1.7)

Debian Science geometry packages

science-highenergy-physics (1.7)

Debian Science High Energy Physics packages

science-highenergy-physics-dev (1.7)

Debian Science High Energy Physics development packages

science-imageanalysis (1.7)

Debian Science image analysis packages

science-linguistics (1.7)

Debian Science Linguistics packages

science-logic (1.7)

Debian Science Logic packages

science-machine-learning (1.7)

Debian Science Machine Learning packages

science-mathematics (1.7)

Debian Science Mathematics packages

science-mathematics-dev (1.7)

Debian Science Mathematics-dev packages

science-meteorology (1.7)

Debian Science Meteorology packages

science-meteorology-dev (1.7)

Debian Science Meteorology-dev packages

science-nanoscale-physics (1.7)

Debian Science Nanoscale Physics packages

science-nanoscale-physics-dev (1.7)

Debian Science Nanoscale Physics development packages

science-neuroscience-cognitive (1.7)

Debian Science packages for Cognitive Neuroscience

science-neuroscience-modeling (1.7)

Debian Science packages for modeling of neural systems

science-numericalcomputation (1.7)

Debian Science Numerical Computation packages

science-physics (1.7)

Debian Science Physics packages

science-physics-dev (1.7)

Debian Science Physics-dev packages

science-presentation (1.7)

Debian Science generic tools for presentations

science-psychophysics (1.7)

Debian Science packages for Psychophysics

science-robotics (1.7)

Debian Robotics packages

science-robotics-dev (1.7)

Debian Robotics development packages

science-simulations (1.7)

Debian Science Simulation packages

science-social (1.7)

Debian Science social sciences packages

science-statistics (1.7)

Debian Science Statistics packages

science-tasks (1.7)

Debian Science tasks for tasksel

science-typesetting (1.7)

Debian Science typesetting packages

science-viewing (1.7)

Debian Science data visualisation packages

science-viewing-dev (1.7)

Debian Science development of visualisation applications

scram (0.11.5-1)

Probabilistic Risk Analysis Tool

scrm (1.7.2-1+b1)

simulator of evolution of genetic sequences

sctk (2.4.10-20151007-1312Z+dfsg2-3)

speech recognition scoring toolkit

scythe (0.994-4)

Bayesian adaptor trimmer for sequencing reads

sdrangelove (0.0.1.20150707-2+b2)

Osmocom Software Defined Radio

seaview (1:4.6.1.2-2)

Multiplatform interface for sequence alignment and phylogeny

seer (1.1.2-3)

genomic sequence element (kmer) enrichment analysis

seq-gen (1.3.3-1+b1 [armhf], 1.3.3-1 [amd64, armel, i386, mips, mipsel, s390x]) [non-free]

simulate the evolution of nucleotide or amino acid sequences

seqan-apps (2.3.1+dfsg-4)

C++ library for the analysis of biological sequences

seqprep (1.3.2-1)

stripping adaptors and/or merging paired reads of DNA sequences with overlap

seqprep-data (1.3.2-1)

example data set for seqprep - only used for testing

seqtk (1.2-1)

Fast and lightweight tool for processing sequences in the FASTA or FASTQ format

sextractor (2.19.5+dfsg-4+b1)

Source extractor for astronomical images

sga (0.10.15-2)

de novo genome assembler that uses string graphs

shelxle (1.0.816-1)

graphical user interface for SHELXL

sibsim4 (0.20-2+b1)

align expressed RNA sequences on a DNA template

sickle (1.33-1+b1)

windowed adaptive trimming tool for FASTQ files using quality

sift (4.0.3b-4) [non-free]

predicts if a substitution in a protein has a phenotypic effect

sigma-align (1.1.3-4+b1)

Simple greedy multiple alignment of non-coding DNA sequences

sigviewer (0.5.1+svn556-5)

GUI viewer for biosignals such as EEG, EMG, and ECG

sim4 (0.0.20121010-4)

tool for aligning cDNA and genomic DNA

sim4db (0~20150903+r2013-3)

batch spliced alignment of cDNA sequences to a target genome

simgrid-java (3.14.159-2)

Java bindings for the SimGrid Toolkit

siril (0.9.5-2)

astronomical image processing tool

skycat (3.1.2+starlink1~b+dfsg-2+b3)

Image visualization and access to catalogs and data for astronomy

slang-xfig (0.2.0~.35-2)

produce plots and drawings through Xfig's fig2dev in S-Lang

sleepyhead (1.0.0-beta-2+dfsg-2+b1)

Sleep tracking software with a focus on monitoring CPAP treatment

smalt (0.7.6-6)

Sequence Mapping and Alignment Tool

smalt-examples (0.7.6-6)

Sequence Mapping and Alignment Tool (examples)

smithwaterman (0.0+20160702-1+b1)

determine similar regions between two strings or genomic sequences

smrtanalysis (0~20161126)

software suite for single molecule, real-time sequencing

snakemake (3.10.0-1)

pythonic workflow management system

snap (2013-11-29-6)

location of genes from DNA sequence with hidden markov model

snap-aligner (1.0~beta.18+dfsg-1)

Scalable Nucleotide Alignment Program

snaphu (1.4.2-2) [non-free]

Statistical-Cost, Network-Flow Algorithm for 2D Phase Unwrapping

sniffles (1.0.2+ds-1)

structural variation caller using third-generation sequencing

snp-sites (2.3.2-1)

Binary code for the package snp-sites

snpomatic (1.0-3+b1)

fast, stringent short-read mapping software

soapdenovo (1.05-3)

short-read assembly method to build de novo draft assembly

soapdenovo2 (240+dfsg1-2)

short-read assembly method to build de novo draft assembly

sortmerna (2.1-1+b1)

tool for filtering, mapping and OTU-picking NGS reads

spaced (1.0.2+dfsg-1+b1)

alignment-free sequence comparison using spaced words

spades (3.9.1+dfsg-1)

genome assembler for single-cell and isolates data sets

spass (3.7-4)

automated theorem prover for first-order logic with equality

spatialite-bin (4.3.0-2+b3)

Geospatial extension for SQLite - tools

spd (1.3.0-1+b2)

Synchrotron image corrections and azimuthal integration

splash (2.6.0-2+b1)

Visualisation tool for Smoothed Particle Hydrodynamics simulation

sprai (0.9.9.22+dfsg-1)

single-pass sequencing read accuracy improver

spread-phy (1.0.7+dfsg-1)

analyze and visualize phylogeographic reconstructions

squizz (0.99c+dfsg-1)

Converter for genetic sequences and alignments

sra-toolkit (2.8.1-2+dfsg-2)

utilities for the NCBI Sequence Read Archive

srst2 (0.2.0-4)

Short Read Sequence Typing for Bacterial Pathogens

ssake (3.8.4-1)

genomics application for assembling millions of very short DNA sequences

ssake-examples (3.8.4-1)

example data for SSAKE, a genomic assembler of short reads

sspace (2.1.1+dfsg-2)

scaffolding pre-assembled contigs after extension

ssw-align (1.1-1+b1)

Smith-Waterman aligner based on libssw

stacks (1.44-2+b1)

pipeline for building loci from short-read DNA sequences

stacks-web (1.44-2)

web interface for displaying loci from short-read sequences

staden (2.0.0+b11-2+b1)

DNA sequence assembly (Gap4/Gap5), editing and analysis tools

staden-common (2.0.0+b11-2)

Architecture independent files for Staden

staden-io-lib-examples (1.14.8-2)

programs for maniuplating DNA sequencing files (usage examples)

staden-io-lib-utils (1.14.8-2)

programs for maniuplating DNA sequencing files

stardata-common (0.8+b1)

Common framework to manage astronomy packages

starplot (0.95.5-8.2+deb9u1)

3-dimensional perspective star map viewer

starpu-contrib-examples (1.2.0+dfsg-4) [contrib]

Task scheduler for heterogeneous multicore machines - exs

starpu-examples (1.2.0+dfsg-4)

Task scheduler for heterogeneous multicore machines - exs

starpu-examples

virtual package provided by starpu-contrib-examples

stellarium (0.15.0-1+b1)

real-time photo-realistic sky generator

stellarium-data (0.15.0-1)

Stellarium data files

step (4:16.08.0-1+b1)

interactive physical simulator for KDE

stiff (2.4.0-2+b1)

convert scientific FITS images to the TIFF format

subread (1.5.1+dfsg-4)

toolkit for processing next-gen sequencing data

subread-data (1.5.1+dfsg-4)

data files for subread package

suitename (0.3.070628-1+b1)

categorize each suite in an RNA backbone

sumaclust (1.0.20-1+b1)

fast and exact clustering of genomic sequences

sumatra (1.0.20-1+b1)

fast and exact comparison and clustering of sequences

sumo (0.28.0+dfsg1-1)

Simulation of Urban MObility (SUMO)

surankco (0.0.r5+dfsg-1)

Supervised Ranking of Contigs in de novo Assemblies

survex (1.2.30-1)

cave surveying and mapping software

survex-aven (1.2.30-1)

sophisticated cave survey viewer for Survex

swarm (2.1.12+dfsg-1)

robust and fast clustering method for amplicon-based studies

swarp (2.38.0+dfsg-3+b1)

Resample and co-add together FITS images

swarp

virtual package provided by suckless-tools

swe-basic-data (1.80.00.0002-1)

basic data files for the libswe package

swe-standard-data (00004-1)

standard data for the Swiss Ephemeris

synphot-data (0.9.8.5+dfsg-1) [contrib]

Optional data files for pysynphot

syrthes (4.3.0-dfsg1-2)

Transient thermal simulations in complex solid geometries

syrthes-gui (4.3.0-dfsg1-2)

Transient thermal simulations in complex solid geometries - GUI

syrthes-tests (4.3.0-dfsg1-2)

Test cases for SYRTHES

syrthes-tools (4.3.0-dfsg1-2)

Transient thermal simulations in complex solid geometries - tools

t-coffee (11.00.8cbe486-5)

Multiple Sequence Alignment

t-coffee-examples (11.00.8cbe486-5)

annotated examples for the use of T-Coffee

tabix (1.3.2-2)

generic indexer for TAB-delimited genome position files

tandem-mass (1:20151215-4+b1)

mass spectrometry software for protein identification

tantan (13-4)

low complexity and tandem repeat masker for biosequences

tcd-utils (20061127-2+b2)

convert Tide Constituent Database (TCD) files

terraintool (1.12a-1)

Generates survex format terrain models from SRTM and ASTER data

tessa (0.3.1-6.2)

simulation of 3D optical systems with the FDTD method

tessa-mpi (0.3.1-6.2)

simulation of 3D optical systems using FDTD on MPI clusters

therion (5.3.16-10+b4)

Cave surveying - 2D and 3D drawing software

therion-viewer (5.3.16-10+b4)

Cave surveying - 3D viewer for therion models

theseus (3.3.0-5+b1)

superimpose macromolecules using maximum likelihood

theseus-examples (3.3.0-5)

superimpose macromolecules using maximum likelihood (examples)

tigr-glimmer (3.02b-1)

Gene detection in archea and bacteria

timbl (6.4.8-1+b1)

Tilburg Memory Based Learner

timblserver (1.11-1+b1)

Server extensions for Timbl

tksao (7.5+repack1-2)

Tk widgets for astronomical imaging and data visualization

tm-align (20160521+dfsg-2)

structural alignment of proteins

tophat (2.1.1+dfsg-2+b2)

fast splice junction mapper for RNA-Seq reads

toppred (1.10-4)

transmembrane topology prediction

transcalc (0.14-6)

microwave and RF transmission line calculator

transdecoder (3.0.1+dfsg-1)

find coding regions within RNA transcript sequences

transrate-tools (1.0.0-1+b1)

helper for transrate

transtermhp (2.09-3+b1)

find rho-independent transcription terminators in bacterial genomes

travis (161013-1)

trajectory analyzer and visualizer

tree-ppuzzle (5.2-8+b3)

Parallelized reconstruction of phylogenetic trees by maximum likelihood

tree-puzzle (5.2-8+b3)

Reconstruction of phylogenetic trees by maximum likelihood

treeview (1.1.6.4+dfsg1-2)

Java re-implementation of Michael Eisen's TreeView

treeviewx (0.5.1+20100823-4)

Displays and prints phylogenetic trees

triangle-bin (1.6-2) [non-free]

High-quality 2-D mesh generator binary programs

trimmomatic (0.36+dfsg-1)

flexible read trimming tool for Illumina NGS data

trinityrnaseq (2.2.0+dfsg-2+b1)

RNA-Seq De novo Assembly

trinityrnaseq-examples (2.2.0+dfsg-2)

RNA-Seq De novo Assembly common example and testing files

tunnelx (20160713-3)

Cave Survey drawing software

twms (0.05t-4)

tiny web map service

ubertooth (2015.09.R2-4)

2.4 GHz wireless development platform for Bluetooth experimentation

ubertooth-firmware (2015.09.R2-4)

Firmware for Ubertooth

ubertooth-firmware-source (2015.09.R2-4)

Source code for the Ubertooth firmware

uc-echo (1.12-9+b1)

error correction algorithm designed for short-reads from NGS

ucto (0.9.6-1)

Unicode Tokenizer

uctodata (0.4-1)

Data files for Ucto

ugene (1.25.0+dfsg-1) [non-free]

integrated bioinformatics toolkit

ugene-data (1.25.0+dfsg-1) [non-free]

required data for UGENE - integrated bioinformatics toolkit

uhd-host (3.9.5-2+b3)

universal hardware driver for Ettus Research products - host apps

units-filter (3.7-3)

Parser for expressions concerning physical values

v-sim (3.7.2-2)

Visualize atomic structures

v-sim-common (3.7.2-2)

Visualize atomic structures (support files)

v-sim-plugins (3.7.2-2)

Plugins for V_Sim (a 3D visualization package)

varna (3-93+ds-1)

Visualization Applet for RNA

varscan (2.4.3+dfsg-1) [non-free]

variant detection in next-generation sequencing data

vcftools (0.1.14+dfsg-4)

Collection of tools to work with VCF files

velvet (1.2.10+dfsg1-3+b1)

Nucleic acid sequence assembler for very short reads

velvet-example (1.2.10+dfsg1-3)

Example data for the Velvet sequence assembler

velvet-long (1.2.10+dfsg1-3+b1)

Nucleic acid sequence assembler for very short reads, long version

velvet-tests (1.2.10+dfsg1-3)

Test data for the Velvet sequence assembler

velvetoptimiser (2.2.5-5)

automatically optimise Velvet do novo assembly parameters

veusz (1.21.1-1.1)

2D scientific plotting application with graphical interface

veusz-helpers (1.21.1-1.1)

Architecture-specific helper module for Veusz

viewmol (2.4.1-24+b1)

graphical front end for computational chemistry programs

visp-images-data (3.0.0-2)

visual servoing library - dataset reference files

vistrails (2.2.4-1)

Science visualisation workflow toolkit

vmtk (1.3+dfsg-2.1+deb9u1) [non-free]

the Vascular Modeling Toolkit

votca-csg (1.3.0-3+b1)

VOTCA's coarse-graining engine

votca-csg-scripts (1.3.0-3)

VOTCA's coarse-graining scripts

votca-csg-tutorials (1.3.0-3)

VOTCA's coarse-graining tutorials

voxbo (1.8.5~svn1246-2+b3)

processing, statistical analysis, and display of brain imaging data

vsearch (2.3.4-1)

tool for processing metagenomic sequences

wcslib-tools (5.16-1)

Command line tools utilizing wcslib

wcstools (3.9.4-2+b1)

Handle the WCS of a FITS image

weightwatcher (1.12-1+b1)

Combine maps and polygon data for astronomical image processing

weka (3.6.14-1)

Machine learning algorithms for data mining tasks

wfrog (0.8.2+svn973-1)

Web-based customizable weather station software

wigeon (20101212+dfsg1-1)

reimplementation of the Pintail 16S DNA anomaly detection utility

wise (2.4.1-19)

comparison of biopolymers, like DNA and protein sequences

wsclean (2.2.1-1)

Fast generic widefield interferometric imager

wxastrocapture (1.8.1+git20140821+dfsg-1+b2)

Windows linuX Astronomy Capture

xbs (0-10+b1)

3-d models and movies of molecules

xcrysden (1.5.60-1+b2)

Crystalline and Molecular Structure Visualizer

xcrysden-data (1.5.60-1)

Crystalline and Molecular Structure Visualizer (Data Files)

xdrawchem (2.0-6)

Chemical structures and reactions editor

xflr5 (6.09.06-2+b3)

analysis tool for airfoils

xfoil (6.99.dfsg-2+b1)

program for the design and analysis of subsonic airfoils

xmakemol (5.16-9+b1)

program for visualizing atomic and molecular systems

xmakemol-gl (5.16-9+b1)

program for visualizing atomic and molecular systems (OpenGL)

xmds2 (2.2.2+dfsg-3)

eXtensible Multi-Dimensional Simulator

xpa-tools (2.1.18-1+b1)

Tools for seamless communication between Unix programs

xplot (1.19-9+b2)

simple on-screen x-y column data plotter

xplot-xplot.org (0.90.7.1-3)

fast tool to graph and visualize lots of data

xppaut (6.11b+1.dfsg-1+b2)

Phase Plane Plus Auto: Solves many kinds of equations

xtide (2.13.2-1+b3)

provides tide and current predictions

xtide-coastline (20020202-1)

coastline data for xtide

xtide-data (20100529-1)

Harmonics data for xtide

xtide-data-nonfree (20100529-1) [non-free]

Harmonics data for xtide (Canada, Netherlands, Germany and UK)

xyscan (3.33-1+b1)

data thief for scientists

yade (2017.01a-8)

Platform for discrete element modeling

yagv (0.4~20130422.r5bd15ed+dfsg-1)

yet another G-code viewer

yale (5.0.95-2) [non-free]

stellar data set from the Yale Bright Star Catalog

yorick (2.2.04+dfsg1-6+b1)

interpreted language and scientific graphics

yorick-av (0.0.4-1)

write movies from Yorick in various formats

yorick-cubeview (2.2-2)

3D FITS data viewer specialized in spectro-imaging

yorick-curses (0.1-6+b1)

interface to the (n)curses library for the Yorick language

yorick-data (2.2.04+dfsg1-6)

interpreted library for the Yorick language

yorick-dev (2.2.04+dfsg1-6+b1)

development files for the Yorick interpreted language

yorick-full (2.2.04+dfsg1-6+b1)

full installation of the Yorick interpreter and add-ons

yorick-gl (1.1+cvs20070922+dfsg-6.1)

OpenGL 3D graphics support for the Yorick language

yorick-gy (0.0.5-1)

GObject introspection and Gtk bindings for Yorick

yorick-gyoto (1.2.0-2)

General relativistic geodesic integration for the Yorick language

yorick-hdf5 (0.8.0-8)

Hierarchical Data Format 5 interface for the Yorick language

yorick-imutil (0.5.7-3)

fast image manipulation routines for the Yorick language

yorick-mira (1.1.0+git20170124.3bd1c3~dfsg1-2)

optical interferometry image reconstruction within Yorick

yorick-ml4 (0.6.0-3)

Matlab file format support for the Yorick language

yorick-mpeg (0.1-3)

MPEG output support for the Yorick language

yorick-mpy-common (2.2.04+dfsg1-6)

Message Passing Yorick (common files)

yorick-mpy-mpich2 (2.2.04+dfsg1-6+b1)

Message Passing Yorick (MPICH2 build)

yorick-mpy-openmpi (2.2.04+dfsg1-6+b1)

Message Passing Yorick (OpenMPI build)

yorick-optimpack (1.3.2+dfsg+1.4.0-1)

optimization of large scale problems for the Yorick language

yorick-soy (1.4.0-3)

sparse matrix operations for the Yorick language

yorick-spydr (0.8.2-3)

FITS image display and simple analysis

yorick-svipc (0.16-2+b2)

interprocess communication (shared memory...) for Yorick

yorick-yao (5.4.0-1)

Yorick-based adaptive optics system simulator

yorick-yeti (6.4.0-1)

utility plugin for the Yorick language

yorick-yeti-fftw (6.4.0-1)

FFT plugin for the Yorick language

yorick-yeti-regex (6.4.0-1)

POSIX regular expressions for the Yorick language

yorick-yeti-tiff (6.4.0-1)

TIFF image format input for the Yorick language

yorick-ygsl (1.2.1-1)

GSL special functions plugin for the Yorick language

yorick-ynfft (1.0.3-1)

nonequispaced fast Fourier transform for Yorick

yorick-yutils (1.5.2-1)

various utilities for the Yorick language

yorick-z (1.2.0+cvs20080115-5+b2 [amd64, arm64, armel, armhf, i386, mips, mipsel, ppc64el, s390x], 1.2.0+cvs20080115-5+b1 [mips64el])

zlib, jpeg and png support for the Yorick language

z3 (4.4.1-0.4~deb9u1)

theorem prover from Microsoft Research

z88 (13.0.0+dfsg2-4+b1)

Finite Element Analysis Program - runtime

z88-data (13.0.0+dfsg2-4)

Finite Element Analysis Program - data

zalign (0.9.1-2+b3)

parallel local alignment of biological sequences

zegrapher (3.0-2)

plotting mathematical functions and sequences on the plane

zimpl (3.3.2-1+b1)

mathematical modeling language for optimization problems

ztex-bmp (20120314-2)

universal macro processor