Software Packages in "ecne", Subsection science

3depict (0.0.23-2build3)

visualisation and analysis for single valued point data

abacas (1.3.1-9)

close gaps in genomic alignments from short reads

abacas-examples (1.3.1-9)

sample data for abacas to close gaps in genomic alignments

abinit (9.10.4-2ubuntu3)

package for electronic structure calculations

abinit-data (9.10.4-2ubuntu3)

package for electronic structure calculations (Data files)

abpoa (1.5.1-1build1)

adaptive banded Partial Order Alignment

abyss (2.3.7-2ubuntu3)

de novo, parallel, sequence assembler for short reads

acedb-other (4.9.39+dfsg.02-9)

retrieval of DNA or protein sequences

aces3 (3.0.8-9build2)

Advanced Concepts in Electronic Structure III

aces3-data (3.0.8-9build2)

Advanced Concepts in Electronic Structure III

achilles (2-12build2)

Artificial life and evolution simulator

adapterremoval (2.3.3-2)

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

adapterremoval-examples (2.3.3-2)

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

adms (2.3.7-1build1)

Automatic device model synthesizer for Verilog-AMS

adun-core (0.81-14build4)

Molecular Simulator

adun.app (0.81-14build4)

Molecular Simulator for GNUstep (GUI)

aegean (0.16.0+dfsg-4)

integrated genome analysis toolkit

aevol (5.0+ds-3)

digital genetics model to run Evolution Experiments in silico

aghermann (1.1.2-5build2)

Sleep-research experiment manager

aladin (12.060+dfsg-3)

Interactive sky atlas for astronomical images and datasets

alfa (2.2-1build3)

Automated Line Fitting Algorithm

algotutor (0.8.6-6)

program for observing the intermediate steps of algorithm

alien-hunter (1.7-10)

Interpolated Variable Order Motifs to identify horizontally acquired DNA

allelecount (4.3.0-2build2)

NGS copy number algorithms

altree (1.3.2-2build3)

program to perform phylogeny-based association and localization analysis

altree-examples (1.3.2-2build3)

example files for ALTree

amap-align (2.2+git20080214.600fc29+dfsg-2)

Protein multiple alignment by sequence annealing

ampliconnoise (1.29-10build2)

removal of noise from 454 sequenced PCR amplicons

andi (0.14-3)

Efficient Estimation of Evolutionary Distances

any2fasta (0.4.2-2)

convert various sequence formats to FASTA

any2fasta-examples (0.4.2-2)

convert various sequence formats to FASTA (example data)

aoflagger (3.4.0-2build4)

Find RFI in radio astronomical observations

apbs (3.4.1-5.1ubuntu2)

Adaptive Poisson Boltzmann Solver

apbs-data (3.4.1-5.1ubuntu2)

data files for APBS (Adaptive Poisson Boltzmann Solver)

apbs-doc (3.4.1-5.1ubuntu2)

Adaptive Poisson Boltzmann Solver

apertium-af-nl (0.3.0-3)

Transitional dummy package for apertium-afr-nld

apertium-afr-nld (0.3.0-3)

Apertium translation data for the Afrikaans-Dutch pair

apertium-all-dev (3.8.1-3)

Metapackage for all tools required for Apertium development

apertium-anaphora (1.1.1-1build2)

Anaphora resolution module for Apertium

apertium-apy (0.11.7-2.1)

Apertium APY service

apertium-arg-cat (0.3.0-2)

Apertium translation data for the Aragonese-Catalan pair

apertium-bel-rus (0.2.1-2)

Apertium translation data for the Belarusian-Russian pair

apertium-br-fr (0.5.1-1)

Apertium linguistic data to translate between Breton and French

apertium-ca-it (1.1.0-1)

Transitional dummy package for apertium-cat-ita

apertium-cat-ita (1.1.0-1)

Apertium translation data for the Catalan-Italian pair

apertium-cat-srd (1.2.0-1)

Apertium translation data for the Catalan-Sardinian pair

apertium-crh-tur (0.3.0-2)

Apertium translation data for the Crimean Tatar-Turkish pair

apertium-cy-en (0.1.1~r57554-9)

Apertium translation data for the Welsh-English pair

apertium-dan-nor (1.5.0-2)

Apertium translation data for the Danish-Norwegian pair

apertium-dev (3.9.4-1build1)

Development tools and library for Apertium

apertium-en-gl (0.5.4-2)

Apertium translation data for the English-Galician pair

apertium-eng-cat (1.0.1-5)

Apertium translation data for the English-Catalan pair

apertium-eng-spa (0.8.1-2)

Apertium translation data for the English-Spanish pair

apertium-eo-en (1.0.2-1)

Apertium linguistic data to translate between Esperanto and English

apertium-eo-fr (0.9.1-1)

Apertium translation data for the Esperanto-French pair

apertium-es-ast (1.1.1-2)

Transitional dummy package for apertium-spa-ast

apertium-es-it (0.2.1-3)

Transitional dummy package for apertium-spa-ita

apertium-eu-en (0.3.3-1)

Apertium translation data for the Basque-English pair

apertium-eval-translator (1.2.1-3)

Evaluate machine translation output against reference

apertium-fra-cat (1.10.0-1)

Apertium translation data for the French-Catalan pair

apertium-fra-frp (1.1.0-1)

Apertium translation data for the French-Arpitan pair

apertium-get (1.0.0-3)

Helper for Apertium and Giellatekno languages and pairs

apertium-hbs-eng (0.5.1-2)

Apertium translation data for the Serbo-Croatian - English pair

apertium-hbs-mkd (0.1.1-1)

Apertium translation data for the Serbo-Croatian-Macedonian pair

apertium-hbs-slv (0.5.1-2)

Apertium translation data for the Serbo-Croatian-Slovenian pair

apertium-hin (0.1.0~r59158-4)

Apertium single language data for Hindi

apertium-id-ms (0.1.2-3)

Transitional dummy package for apertium-ind-zlm

apertium-ind-zlm (0.1.2-3)

Apertium translation data for the Indonesian-Malay pair

apertium-is-sv (0.1.1-2)

Transitional dummy package for apertium-isl-swe

apertium-isl-eng (0.1.2-1)

Apertium translation data for the Icelandic-English pair

apertium-isl-swe (0.1.1-2)

Apertium translation data for the Icelandic-Swedish pair

apertium-kaz-tat (0.2.1-1)

Apertium translation data for the Kazakh-Tatar pair

apertium-lex-tools (0.4.2-2build3)

Constraint-based lexical selection module

apertium-lex-tools-dev (0.4.2-2build3)

Development library for Apertium lexical selection module

apertium-mk-bg (0.2.1-2)

Transitional dummy package for apertium-mkd-bul

apertium-mk-en (0.1.3-2)

Transitional dummy package for apertium-mkd-eng

apertium-mkd-bul (0.2.1-2)

Apertium translation data for the Macedonian-Bulgarian pair

apertium-mkd-eng (0.1.3-2)

Apertium translation data for the Macedonian-English pair

apertium-mlt-ara (0.2.0~r62623-3)

Apertium translation data for the Maltese-Arabic pair

apertium-nno-nob (1.5.0-1)

Apertium translation data for the Norwegian Nynorsk-Norwegian Bokmål pair

apertium-oci-fra (1.0.0-1)

Apertium translation data for the Occitan-French pair

apertium-pol-szl (0.2.1-3)

Apertium translation data for the Polish-Silesian pair

apertium-por-cat (0.10.1-2)

Apertium translation data for the Portuguese-Catalan pair

apertium-recursive (1.1.2-1build2)

Apertium recursive structural transfer module

apertium-regtest (0.9.1-3)

Regression test suite for Apertium languages and pairs

apertium-rus-ukr (0.2.1-4)

Apertium translation data for the Russian-Ukrainian pair

apertium-separable (0.6.1-1build2)

Reordering separable/discontiguous multiwords

apertium-sme-nob (0.6.1+ds.1-2)

Apertium translation data for the Northern Sami-Norwegian Bokmål pair

apertium-spa-arg (0.6.0-2)

Apertium translation data for the Spanish-Aragonese pair

apertium-spa-ast (1.1.1-2)

Apertium translation data for the Spanish-Asturian pair

apertium-spa-ast

virtual package provided by apertium-spa-ast

apertium-spa-cat (2.2.0-3)

Apertium translation data for the Spanish-Catalan pair

apertium-spa-ita (0.2.1-3)

Apertium translation data for the Spanish-Italian pair

apertium-srd-ita (1.3.0-1)

Apertium translation data for the Sardinian-Italian pair

apertium-swe-dan (0.8.1-3)

Apertium translation data for the Swedish-Danish pair

apertium-swe-nor (0.4.0-1)

Apertium translation data for the Swedish-Norwegian pair

apertium-urd (0.1.0~r61311-3)

Apertium single language data for Urdu

apertium-urd-hin (0.1.0~r64379-4)

Apertium translation data for the Urdu-Hindi pair

aragorn (1.2.41-2)

tRNA and tmRNA detection in nucleotide sequences

arden (1.0-5)

specificity control for read alignments using an artificial reference

ariba (2.14.7+ds-2build1)

Antibiotic Resistance Identification By Assembly

art-nextgen-simulation-tools (20160605+dfsg-5)

simulation tools to generate synthetic next-generation sequencing reads

art-nextgen-simulation-tools-profiles (20160605+dfsg-5)

profiles for art simulation tools

artemis (18.2.0+dfsg-3)

genome browser and annotation tool

artfastqgenerator (0.0.20150519-5)

outputs artificial FASTQ files derived from a reference genome

artfastqgenerator-examples (0.0.20150519-5)

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

asdftool (3.1.0-1)

Command line tool to manipulate ASDF scientific data files

ase (3.22.1-4)

Atomic Simulation Environment

assembly-stats (1.0.1+ds-6)

get assembly statistics from FASTA and FASTQ files

assemblytics (1.2.1+dfsg-2)

detect and analyze structural variants from a genome assembly

astap (2024.01.16-1)

astrometric (plate) solver, stacking of images, photometry and FITS viewer

astap-cli (2024.01.17-1)

astrometric (plate) solver, command line version

astro-tasks (4.1)

Debian Astronomy Pure Blend (tasksel tasks)

astromatic (1.3)

Astronomical pipeline software collection

astrometry-data-tycho2 (2-4)

Astrometry.net Tycho-2 index files

astrometry-data-tycho2-07 (2-4)

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

astrometry-data-tycho2-07-bigendian (2-4)

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

astrometry-data-tycho2-07-littleendian (2-4)

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

astrometry-data-tycho2-08 (2-4)

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

astrometry-data-tycho2-08-bigendian (2-4)

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

astrometry-data-tycho2-08-littleendian (2-4)

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

astrometry-data-tycho2-09 (2-4)

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

astrometry-data-tycho2-09-bigendian (2-4)

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

astrometry-data-tycho2-09-littleendian (2-4)

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

astrometry-data-tycho2-10-19 (2-4)

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

astrometry-data-tycho2-10-19-bigendian (2-4)

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

astrometry-data-tycho2-10-19-littleendian (2-4)

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

astrometry.net (0.93+dfsg-1.1ubuntu1)

Astrometry plate solver

astronomical-almanac (5.6-7)

astronomical almanac - calculate planet and star positions

atac (0~20150903+r2013-8build4)

genome assembly-to-assembly comparison

ataqv (1.3.1+ds-2build3)

ATAC-seq QC and visualization

atomes (1.1.12+repack-2ubuntu2)

atomic-scale 3D modeling toolbox

atomes-data (1.1.12+repack-2ubuntu2)

atomic-scale 3D modeling toolbox (data)

atropos (1.1.32+dfsg-1build1)

NGS read trimming tool that is specific, sensitive, and speedy

augur (24.2.2-1)

pipeline components for real-time virus analysis

augustus (3.5.0+dfsg-4build5)

gene prediction in eukaryotic genomes

augustus-data (3.5.0+dfsg-4build5)

data files for AUGUSTUS

autodock (4.2.6-9)

analysis of ligand binding to protein structure

autodock-getdata (4.2.6-9)

instructions for getData to collect compounds

autodock-test (4.2.6-9)

test files for AutoDock

autodock-vina (1.2.5-2build1)

docking of small molecules to proteins

autogrid (4.2.6-9)

pre-calculate binding of ligands to their receptor

autogrid-test (4.2.6-9)

test files for AutoGrid

avce00 (2.0.0-9)

Conversion of ESRI Arcinfo Vector Coverage in E00 format

avogadro (1.99.0-1build2)

Molecular Graphics and Modelling System

avogadro-utils (1.99.0-5build2)

Molecular Graphics and Modelling System (library)

axe-demultiplexer (0.3.3+dfsg-4build1)

Trie-based DNA sequencing read demultiplexer

bagel (1.2.2-7)

Computational Chemistry Package

baitfisher (1.2.7+git20211020.de26d5c+dfsg-1)

software package for designing hybrid enrichment probes

bali-phy (3.6.1+dfsg-2build3)

Bayesian Inference of Alignment and Phylogeny

ballview (1.5.0+git20180813.37fc53c-11build5)

free molecular modeling and molecular graphics tool

bamclipper (1.0.0-3)

Remove gene-specific primer sequences from SAM/BAM alignments

bamkit (0.0.1+git20170413.ccd079d-3)

tools for common BAM file manipulations

bamtools (2.5.2+dfsg-4)

toolkit for manipulating BAM (genome alignment) files

bandage (0.9.0-2build2)

Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bandage-examples (0.9.0-2build2)

Bioinformatics Application for Navigating De novo Assembly Graphs Easily (data)

barrnap (0.9+dfsg-4)

rapid ribosomal RNA prediction

bart (0.9.00-2build2)

tools for computational magnetic resonance imaging

bart-view (0.3.00-1build3)

viewer for multi-dimensional complex-valued data

bbmap (39.06+dfsg-1)

BBTools genomic aligner and other tools for short sequences

bbmap-jni (39.06+dfsg-1)

short read aligner and other bioinformatic tools - JNI library

bcalm (2.2.3-5build2)

de Bruijn compaction in low memory

bcftools (1.19-1build2)

genomic variant calling and manipulation of VCF/BCF files

beads (1.1.22-1build4)

2-DE electrophoresis gel image spot detection

beagle (220722-1)

Genotype calling, genotype phasing and imputation of ungenotyped markers

beast2-mcmc (2.7.6+dfsg-1)

Bayesian MCMC phylogenetic inference

bedops (2.4.41+dfsg-2build1)

high-performance genomic feature operations

bedtools (2.31.1+dfsg-2)

suite of utilities for comparing genomic features

bedtools-test (2.31.1+dfsg-2)

test data for the bedtools package

belvu (4.44.1+dfsg-7.1build2)

multiple sequence alignment viewer and phylogenetic tool

berkeley-express (1.5.3+dfsg-3build5)

Streaming quantification for high-throughput sequencing

bio-eagle (2.4.1-3build2)

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

bio-eagle-examples (2.4.1-3build2)

Examples for bio-eagle

bio-rainbow (2.0.4+dfsg-2)

clustering and assembling short reads for bioinformatics

bio-vcf (0.9.5-3)

domain specific language (DSL) for processing the VCF format

bioawk (1.0-4)

extension of awk for biological sequence analysis

biobambam2 (2.0.185+ds-1)

tools for early stage alignment file processing

biogenesis (0.8-3.1)

artificial life program that simulates evolution of organisms

bioperl (1.7.8-1)

Perl tools for computational molecular biology

bioperl-run (1.7.3-9)

BioPerl wrappers: scripts

biosig-tools (2.6.0-1ubuntu1)

format conversion tools for biomedical data formats

biosquid (1.9g+cvs20050121-15.1build1)

utilities for biological sequence analysis

biosyntax (1.0.0b-6)

Syntax Highlighting for Computational Biology (metapackage)

biosyntax-common (1.0.0b-6)

Syntax Highlighting for Computational Biology (common files)

biosyntax-example (1.0.0b-6)

Syntax Highlighting for Computational Biology (example)

biosyntax-gedit (1.0.0b-6)

Syntax Highlighting for Computational Biology (gedit)

biosyntax-less (1.0.0b-6)

Syntax Highlighting for Computational Biology (less)

biosyntax-vim (1.0.0b-6)

Syntax Highlighting for Computational Biology (vim)

bitseq (0.7.5+dfsg-6)

Bayesian Inference of Transcripts from Sequencing Data

bitwise (0.50-1build1)

Interactive bitwise operation in ncurses

bkchem (0.14.0~pre4+git20211228-3)

Chemical structures editor

blasr (5.3.5+dfsg-6build5)

mapping single-molecule sequencing reads

blinken (4:23.08.5-0ubuntu4)

KDE version of the Simon electronic memory game

blixem (4.44.1+dfsg-7.1build2)

interactive browser of sequence alignments

bluebrain-hpc-coding-conventions (1.0.0+git20221201-2)

BlueBrain HPC Team C++ Development Guidelines

bmt (0.6-1.1)

software analysis benchmarking toolkit

bodr (10-3)

Blue Obelisk Data Repository

bolt-lmm (2.4.1+dfsg-2)

Efficient large cohorts genome-wide Bayesian mixed-model association testing

bolt-lmm-example (2.4.1+dfsg-2)

Examples for bolt-lmm

boolector (1.5.118.6b56be4.121013-1.3)

SMT solver for bit-vectors and arrays

bornagain (21.1+ds3-4)

Simulate and fit X-ray and neutron GISAS -- binary

bowtie (1.3.1-3)

Ultrafast memory-efficient short read aligner

bowtie-examples (1.3.1-3)

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

bowtie2 (2.5.2-1)

ultrafast memory-efficient short read aligner

bowtie2-examples (2.5.2-1)

Examples for bowtie2

boxshade (3.3.1-14)

Pretty-printing of multiple sequence alignments

bppphyview (0.6.1-4build3)

Bio++ Phylogenetic Viewer

bppsuite (2.4.1-6build3)

Bio++ program suite

bppsuite-examples (2.4.1-6build3)

Examples for Bio++ program suite

brig (0.95+dfsg-3)

BLAST Ring Image Generator

btllib-tools (1.4.10+dfsg-1ubuntu2)

Bioinformatics Technology Lab common code library tools

busco (5.5.0-2)

benchmarking sets of universal single-copy orthologs

bustools (0.43.2+dfsg-1)

program for manipulating BUS files for single cell RNA-Seq datasets

bwa (0.7.17-7)

Burrows-Wheeler Aligner

c-munipack (2.1.36-2build2)

reduction of images carried out by CCD camera

c-munipack-share (2.1.36-2build2)

reduction of images carried out by CCD camera (share)

c2x (2.41.b+ds-2)

converter between DFT electronic structure codes formats

cafeobj (1.6.0-2build1)

new generation algebraic specification and programming language

cafeobj-mode (1.6.0-2build1)

Emacs major mode for editing CafeOBJ source code

calculix-ccx (2.21-1)

Three-Dimensional Structural Finite Element Program

calculix-cgx (2.21+dfsg-1build1)

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

callisto (1.1.0-2build4)

Daemon for e-Callisto hardware

camitk-actionstatemachine (5.2.0-1build7)

pipeline replay application for the CamiTK library

camitk-config (5.2.0-1build7)

Computer Assisted Medical Intervention Tool Kit - config

camitk-imp (5.2.0-1build7)

workbench application for the CamiTK library

canu (2.2+dfsg-5)

single molecule sequence assembler for genomes

casacore-data-igrf (12-1)

International Geomagnetic Reference Field data for casacore

casacore-data-jpl-de200 (2007.07.05+ds.1-1)

Jet Propulsion Laboratory Development Ephemeris DE200 for casacore

casacore-data-jpl-de405 (2007.07.05+ds.1-1)

Jet Propulsion Laboratory Development Ephemeris DE405 for casacore

casacore-data-lines (0+git2016.11.26-2.1)

Table of spectral line frequencies for casacore

casacore-data-observatories (0+git2018.12.08-2)

Table of radio observatory coordinates for casacore

casacore-data-sources (2-4)

Table of ICRF reference source coordinates for casacore

casacore-data-tai-utc (1.3)

Difference table between TAI and UTC for casacore

casacore-tools (3.5.0-4.1ubuntu2)

Tools built with CASA

cassbeam (1.1-4build2)

Cassegrain antenna modelling

cassiopee (1.0.9-4build3)

index and search tool in genomic sequences

cat-bat (5.3-2)

taxonomic classification of contigs and metagenome-assembled genomes (MAGs)

catfishq (1.4.0+ds-1)

concatenates fastq files

cba (0.3.6-6build3)

Continuous Beam Analysis

cbflib-bin (0.9.7+dfsg1-3.1build2)

utilities to manipulate CBF files

cbmc (5.95.1-4ubuntu1 [amd64, ppc64el, riscv64], 5.12-5 [arm64, armhf])

bounded model checker for C and C++ programs

cclib (1.8-1)

Parsers and algorithms for computational chemistry

cct (1:1.0.3-1)

visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences

cct-examples (1:1.0.3-1)

example data for testing the package cct

cd-hit (4.8.1-4)

suite of programs designed to quickly group sequences

cdbfasta (1.00+git20230710.da8f5ba+dfsg-1build1)

Constant DataBase indexing and retrieval tools for multi-FASTA files

centrifuge (1.0.3-12build1)

rapid and memory-efficient system for classification of DNA sequences

cg3 (1.4.6-1build2)

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

cg3-dev (1.4.6-1build2)

Metapackage providing both CG-3 CLI dev tools and dev library

cgns-convert (3.4.0-4)

CFD General Notation System - Conversion tools

cgview (0.0.20100111-7)

Circular Genome Viewer

changeo (1.3.0-1)

Repertoire clonal assignment toolkit (Python 3)

checkit-tiff (1.4.4-1)

conformance checker for baseline TIFFs

chemical-structures (2.2.dfsg.0-20)

web service providing molecular structures in open formats

chemical-structures-data (2.2.dfsg.0-20)

set of molecular structures in open formats

chemonomatopist (0.6.1-1)

derive IUPAC systematic names for chemical structures

chemps2 (1.8.12-3.1build2)

Executable to call libchemps2-3t64 from the command line

chemtool (1.6.14-6build2)

chemical structures drawing program

chimeraslayer (20101212+dfsg1-6)

detects likely chimeras in PCR amplified DNA

chip-seq (1.5.5-3)

tools performing common ChIP-Seq data analysis tasks

chip-seq-data (1.5.5-3)

tools performing common ChIP-Seq data analysis tasks (data)

chromhmm (1.25+dfsg-1)

Chromatin state discovery and characterization

chromimpute (1.0.3+dfsg-5)

Large-scale systematic epigenome imputation

cif-linguist (0.4.2-5build1)

transform CIF data among CIF formats and dialects

cif-tools (1.0.7-1)

Suite of tools to manipulate, validate and query mmCIF files

cif2hkl (1.4.3+ds1-1)

Convert crystallographic descriptions into HKL F^2 reflection lists

circlator (1.5.6-11)

circularize genome assemblies

circos (0.69.9+dfsg-2)

plotter for visualizing data

circos-tools (0.23-1)

plotter for visualizing data - helper utilities

ckon (0.7.1-5build4)

automatic build tool for ROOT data analysis software

clearcut (1.0.9+git20211013.b799afe-1)

extremely efficient phylogenetic tree reconstruction

clonalframe (1.2-11build1)

inference of bacterial microevolution using multilocus sequence data

clonalframeml (1.13-1)

Efficient Inference of Recombination in Whole Bacterial Genomes

clonalorigin (1.0-8)

inference of homologous recombination in bacteria using whole genome sequences

clustalo (1.2.4-8build1)

General-purpose multiple sequence alignment program for proteins

clustalw (2.1+lgpl-7)

global multiple nucleotide or peptide sequence alignment

cmor-tables (3.3-1.1)

MIP tables for the Climate Model Output Rewriter library

cmtk (3.3.1p2+dfsg-2build3)

Computational Morphometry Toolkit

cnvkit (0.9.10-1)

Copy number variant detection from targeted DNA sequencing

cod-tools (3.8.1+dfsg-1build3)

tools for manipulating CIF format files

code-saturne (6.0.2-2build2)

General purpose Computational Fluid Dynamics (CFD) software

code-saturne-bin (6.0.2-2build2)

General purpose Computational Fluid Dynamics (CFD) software - binaries

code-saturne-data (6.0.2-2build2)

General purpose Computational Fluid Dynamics (CFD) software - data

code-saturne-include (6.0.2-2build2)

General purpose Computational Fluid Dynamics (CFD) software - includes

codonw (1.4.4-8)

Correspondence Analysis of Codon Usage

coinor-cbc (2.10.11+ds1-2)

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

coinor-clp (1.17.9+ds-1)

Coin-or linear programming solver

coinor-csdp (6.2.0-5build1)

Software package for semidefinite programming (binaries)

coinor-libbonmin4t64 (1.8.9-1.1build1)

COIN-OR mixed integer programming

coinor-libcbc3.1 (2.10.11+ds1-2)

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

coinor-libcgl1 (0.60.8+ds-1)

COIN-OR Cut Generation Library

coinor-libclp1 (1.17.9+ds-1)

Coin-or linear programming solver (shared libraries)

coinor-libcoinutils3v5 (2.11.4+repack1-4)

COIN-OR collection of utility classes (shared libraries)

coinor-libosi1v5 (0.108.9+ds-1)

COIN-OR Open Solver Interface

coinor-libsymphony3 (5.6.17+dfsg-1)

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

coinor-libvol1 (1.5.4-4)

Coin-or linear programming solver (libraries)

coinor-symphony (5.6.17+dfsg-1)

COIN-OR solver for mixed-integer linear programs

colmap (3.9.1-2build2)

Structure-from-Motion and Multi-View Stereo

comet-ms (2019015+cleaned1-4.1)

Tandem mass spectrometry (MS/MS) search engine

concavity (0.1+dfsg.1-5)

predictor of protein ligand binding sites from structure and conservation

conda-package-handling (2.2.0-2)

create and extract conda packages of various formats

condor (23.4.0+dfsg-1ubuntu4)

distributed workload management system

condor-annex-ec2 (23.4.0+dfsg-1ubuntu4)

distributed workload management system - single node configuration

condor-kbdd (23.4.0+dfsg-1ubuntu4)

distributed workload management system - single node configuration

condor-test (23.4.0+dfsg-1ubuntu4)

distributed workload management system - single node configuration

condor-upgrade-checks (23.4.0+dfsg-1ubuntu4)

distributed workload management system - single node configuration

condor-vm-gahp (23.4.0+dfsg-1ubuntu4)

distributed workload management system - single node configuration

connectome-workbench (1.5.0-2build2)

brain visualization, analysis and discovery tool

conservation-code (20110309.0-8)

protein sequence conservation scoring tool

covtobed (1.3.5+dfsg-2)

convert the coverage track from a BAM file into a BED file

covtobed-examples (1.3.5+dfsg-2)

example data and scripts for mindthegap

cpl-plugin-amber (4.4.3+dfsg-1build3)

ESO data reduction pipeline for the AMBER instrument

cpl-plugin-amber-calib (4.4.3+dfsg-1build3)

ESO data reduction pipeline calibration data downloader for AMBER

cpl-plugin-fors (5.5.7+dfsg-2build1)

ESO data reduction pipeline for the FORS1/2 instruments

cpl-plugin-fors-calib (5.5.7+dfsg-2build1)

ESO data reduction pipeline calibration data downloader for FORS2

cpl-plugin-giraf (2.16.10+dfsg-1build3)

ESO data reduction pipeline for the GIRAFFE instrument

cpl-plugin-giraf-calib (2.16.10+dfsg-1build3)

ESO data reduction pipeline calibration data downloader for GIRAFFE

cpl-plugin-hawki (2.4.11+dfsg-1)

ESO data reduction pipeline for the HAWK-I instrument

cpl-plugin-hawki-calib (2.4.11+dfsg-1)

ESO data reduction pipeline calibration data downloader for HAWK-I

cpl-plugin-muse (2.8.7+dfsg-3)

ESO data reduction pipeline for the MUSE instrument

cpl-plugin-muse-calib (2.8.7+dfsg-3)

ESO data reduction pipeline calibration data downloader for MUSE

cpl-plugin-naco (4.4.11+dfsg-1)

ESO data reduction pipeline for the NaCo instrument

cpl-plugin-naco-calib (4.4.11+dfsg-1)

ESO data reduction pipeline NaCo calibration data downloader

cpl-plugin-uves (6.1.8+dfsg-2build3)

ESO data reduction pipeline for the UVES instrument

cpl-plugin-uves-calib (6.1.8+dfsg-2build3)

ESO data reduction pipeline calibration data downloader for UVES

cpl-plugin-vimos (4.1.7+dfsg-2build3)

ESO data reduction pipeline for the VIMOS instrument

cpl-plugin-vimos-calib (4.1.7+dfsg-2build3)

ESO data reduction pipeline calibration data downloader for VIMOS

cpl-plugin-visir (4.4.2+dfsg-1)

ESO data reduction pipeline for the VISIR instrument

cpl-plugin-visir-calib (4.4.2+dfsg-1)

ESO data reduction pipeline calibration data downloader for VISIR

cpl-plugin-xshoo (3.5.3+dfsg-1build4)

ESO data reduction pipeline for the XSHOOTER instrument

cpl-plugin-xshoo-calib (3.5.3+dfsg-1build4)

ESO data reduction pipeline calibration data downloader for XSHOOTER

cpptraj (5.1.0+dfsg-3build3)

fast, parallelized molecular dynamics trajectory data analysis

cpuinfo (0.0~git20230113.6481e8b-2)

CPU INFOrmation library (binary utilities)

crac (2.5.2+dfsg-6build1)

integrated RNA-Seq read analysis

critterding (1.0-beta12.1-1.3build1)

Evolving Artificial Life

ctdconverter (2.1-6)

Convert CTD files into Galaxy tool and CWL CommandLineTool files

ctffind (4.1.14-2build2)

fast and accurate defocus estimation from electron micrographs

ctsim (6.0.2-6build3)

Computed tomography simulator

ctsim-help (6.0.2-6build3)

Online help file for CTSim

cutadapt (4.4-1build2)

Clean biological sequences from high-throughput sequencing reads

cutesv (2.1.0-2)

comprehensive discovery of structural variations of genomic sequences

cwl-upgrader (1.2.11-1)

Common Workflow Language standalone document upgrader

cwlformat (2022.02.18-2)

code formatter for Common Workflow Language

cwltest (2.4.20240129145612-1)

Common Workflow Language testing framework

cwltool (3.1.20240112164112-2)

Common Workflow Language reference implementation

daligner (1.0+git20240119.335105d-2)

local alignment discovery between long nucleotide sequencing reads

damapper (0.0+git20210330.ab45103-2)

long read to reference genome mapping tool

darknet (0.0.0+git20180914.61c9d02e-2build7)

Open Source Neural Networks in C

dascrubber (1.1-4)

alignment-based scrubbing pipeline for DNA sequencing reads

datalad (0.19.6-1)

data files management and distribution platform

datalad-container (1.2.5-1)

DataLad extension for working with containerized environments

dawg (1.2-4)

simulate the evolution of recombinant DNA sequences

dazzdb (1.0+git20230919.414ad05-2build1)

manage nucleotide sequencing read data

dcm2niix (1.0.20220720-1build1)

next generation DICOM to NIfTI converter

dcmtk (3.6.7-9.1build4)

OFFIS DICOM toolkit command line utilities

debian-astro-logo (4.1)

Debian Astronomy Pure Blends Logo

deblur (1.1.1-1)

deconvolution for Illumina amplicon sequencing

delly (1.1.8-1build3)

Structural variant discovery by read analysis

density-fitness (1.0.8-4)

Calculates per-residue electron density scores

dextractor (1.0-6build2)

(d)extractor and compression command library

dh-r (20231212ubuntu1)

Debian helper tools for packaging R libraries

dialign (2.2.1-12build1)

Segment-based multiple sequence alignment

dialign-tx (1.0.2-15build1)

Segment-based multiple sequence alignment

dialign-tx-data (1.0.2-15build1)

Segment-based multiple sequence alignment (data files)

dials (3.17.0+dfsg3-3build3)

Diffraction Integration for Advanced Light Sources

diamond-aligner (2.1.9-1)

accelerated BLAST compatible local sequence aligner

dicomnifti (2.33.1-5build3)

converts DICOM files into the NIfTI format

dimbl (0.15-2.1build3)

Distributed Memory Based Learner

discosnp (1:2.6.2-3build2)

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

disulfinder (1.2.11-12)

cysteines disulfide bonding state and connectivity predictor

disulfinder-data (1.2.11-12)

data files for predictor of disulfide bonds in proteins

dlmodelbox (1.1.1-1)

Swiss Army Knife of Deep Learning Models

dmrgpp (6.06-1build2)

Density matrix renormalization group algorithm

dnaclust (3-7build3)

tool for clustering millions of short DNA sequences

dnapi (1.1-3)

adapter prediction for small RNA sequencing - utils

dnarrange (1.5.3-1)

Method to find rearrangements in long DNA reads relative to a genome seq

dotter (4.44.1+dfsg-7.1build2)

detailed comparison of two genomic sequences

dozzaqueux (3.51-4)

simulator for chemical mixtures

dozzaqueux-data (3.51-4)

databases for chemical mixtures

dpuser (4.1+dfsg-2build3)

Interactive language for handling numbers, strings, and matrices

drawxtl (5.5-6.1build2)

crystal structure viewer

drop-seq-testdata (2.5.4+dfsg-1)

analyzing Drop-seq data (testdata)

drop-seq-tools (2.5.4+dfsg-1)

analyzing Drop-seq data

drs4eb (5.0.6+git20211217+ds-3build2)

DRS4 Evaluation Board software

drslib (0.3.1.p3-2.1)

Command-line tools for the Data Reference Syntax library

dsdp (5.8-10.1build1)

Software for Semidefinite Programming

dssp (4.2.2-2)

protein secondary structure assignment based on 3D structure

dwgsim (0.1.14-2)

short sequencing read simulator

dx (1:4.4.4-15.1build2 [amd64, arm64, ppc64el, riscv64], 1:4.4.4-15.1build1 [armhf])

OpenDX (IBM Visualization Data Explorer) - main package

dxf2gcode (20191025-2)

prepares drawings of parts for automatic machine tools

dxsamples (4.4.0-5)

Sample programs for the OpenDX Data Explorer

dyssol (1.1.1+ds1-2.1build4)

Tool for dynamic flowsheet simulation. Command line tool

dyssol-data (1.1.1+ds1-2.1build4)

Tool for dynamic flowsheet simulation. Data files

dyssol-gui (1.1.1+ds1-2.1build4)

Tool for dynamic flowsheet simulation. GUI

e-mem (1.0.1-5)

Efficient computation of Maximal Exact Matches for very large genomes

e00compr (1.0.1-7)

Program to read/write Arcinfo compressed E00 files

ea-utils (1.1.2+dfsg-9build1)

command-line tools for processing biological sequencing data

easychem (0.6-9build2)

Draw high-quality molecules and 2D chemical formulas

ecaccess (4.0.1-1.1)

clients to access ECMWF facilities

ecflow-client (5.12.0-1build3)

Client tools for Meteorological workflow

ecflow-server (5.12.0-1build3)

Meteorological workflow controller - server

ecopcr (1.0.1+dfsg-4)

estimate PCR barcode primers quality

ectrans-utils (1.3.0-2 [amd64], 1.1.0-4 [arm64, ppc64el, riscv64])

Spherical Harmonics Transforms library - utilities

edfbrowser (2.06+dfsg-1build2)

viewer for biosignal storage files such as bdf and edf

edlib-aligner (1.2.7-5build1)

edlib sequence alignment tool using edit distance

edtsurf (0.2009-10)

triangulated mesh surfaces for protein structures

eigensoft (8.0.0+dfsg-2)

reduction of population bias for genetic analyses

elastix (5.1.0-1)

toolbox for rigid and nonrigid registration of images

elk-lapw (9.2.12-1build2)

All-Electron Density-Functional Electronic Structure Code

elki (0.7.1-10.1)

Data mining algorithm development framework

elki-dev (0.7.1-10.1)

Data mining algorithm development framework - development files

elph (1.0.1-5)

DNA/protein sequence motif finder

embassy-domainatrix (0.1.660-4)

Extra EMBOSS commands to handle domain classification file

embassy-domalign (0.1.660-4)

Extra EMBOSS commands for protein domain alignment

embassy-domsearch (1:0.1.660-3)

Extra EMBOSS commands to search for protein domains

emboss (6.6.0+dfsg-12ubuntu2)

European molecular biology open software suite

emboss-data (6.6.0+dfsg-12ubuntu2)

data files for the EMBOSS package

emboss-explorer (2.2.0-12)

web-based GUI to EMBOSS

emmax (0~beta.20100307-5)

genetic mapping considering population structure

engauge-digitizer (12.1+ds.1-1build3)

interactively extracts numbers from bitmap graphs or maps

ent (1.2debian-3)

pseudorandom number sequence test program

epics-base (7.0.7+dfsg1-5)

EPICS tools

ergo (3.8-1build1)

Quantum chemistry program for large-scale calculations

ergo-data (3.8-1build1)

Quantum chemistry program for large-scale calculations - data package

eso-pipelines (1.3)

ESO VLT Instrument pipeline collection

esorex (3.13.7+ds-1)

Execution Tool for European Southern Observatory pipelines

estscan (3.0.3-6)

ORF-independent detector of coding DNA sequences

esys-particle (2.3.5+dfsg2-6build5)

Software for particle-based numerical modelling (MPI version)

etsf-io (1.0.4-5build1)

Binary tools to check, merge and read ETSF files

examl (3.0.22-4build2)

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference

exonerate (2.4.0-5build2)

generic tool for pairwise sequence comparison

expeyes (5.3.1+repack-6build1)

hardware & software framework for developing science experiments

expeyes-clib (5.3.1+repack-6build1)

hardware & software framework for developing science experiments

eye (22.1201.1601~ds-1)

semantic web reasoning engine

eyes17 (5.3.1+repack-6build1)

hardware & software framework for developing science experiments

eyes17-manuals-en (5.3.1+repack-1)

Eyes17 User Manuals (English version)

eyes17-manuals-es (5.3.1+repack-1)

Eyes17 User Manuals (Spanish version)

eyes17-manuals-fr (5.3.1+repack-1)

Eyes17 User Manuals (French version)

eyes17-manuals-ml (5.3.1+repack-1)

Eyes17 User Manuals (Malayalam version)

fast5 (0.6.5-7build5)

utilities for manipulating Oxford Nanopore Fast5 files

fastahack (1.0.0+dfsg-11)

utility for indexing and sequence extraction from FASTA files

fastani (1.33-3)

Fast alignment-free computation of whole-genome Average Nucleotide Identity

fastaq (3.17.0-6)

FASTA and FASTQ file manipulation tools

fastdnaml (1.2.2-16)

Tool for construction of phylogenetic trees of DNA sequences

fastlink (4.1P-fix100+dfsg-5)

faster version of pedigree programs of Linkage

fastlink-doc (4.1P-fix100+dfsg-5)

Some papers about fastlink

fastml (3.11-4)

maximum likelihood ancestral amino-acid sequence reconstruction

fastp (0.23.4+dfsg-1)

Ultra-fast all-in-one FASTQ preprocessor

fastq-pair (1.0-3)

Rewrites paired end fastq so all reads have a mate to separate out singletons

fastqc (0.12.1+dfsg-3)

quality control for high throughput sequence data

fastqtl (2.184+v7+dfsg-4build3)

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

fasttext (0.9.2+ds-7build1)

Efficient learning of word representations and sentence classification library

fasttree (2.1.11-2)

phylogenetic trees from alignments of nucleotide or protein sequences

fcc (2.16-1)

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

feedgnuplot (1.62-1)

Pipe-oriented frontend to Gnuplot

feff85exafs (0.2+dfsg-2)

Open Source theoretical EXAFS calculations

ffindex (0.9.9.9-6.1build2)

simple index/database for huge amounts of small files

fiat-utils (1.2.0-3build2 [amd64], 1.2.0-1 [arm64, ppc64el, riscv64])

Fortran IFS and Arpege Toolkit - utilities

figtree (1.4.4-6)

graphical phylogenetic tree viewer

filtlong (0.2.1-4)

quality filtering tool for long reads of genome sequences

filtlong-data (0.2.1-4)

quality filtering tool for long reads of genome sequences (testdata)

finalcif (134+dfsg-1)

editor for Crystallographic Information Format

firm-phoenix-ware (4.7.5+repack-2)

firmware necessary for boxes issued by project PHOENIX

fitgcp (0.0.20150429-5)

fitting genome coverage distributions with mixture models

fitscut (1.4.4-6build2)

Extract cutouts from FITS image format files

fitsh (0.9.4-1)

Software package for astronomical image processing

fitspng (2.0-2build3)

FITS to PNG converter

fitsverify (4.22-1build2)

FITS File Format-Verification Tool

fityk (1.3.2-3build3)

general-purpose nonlinear curve fitting and data analysis

flash (1.2.11-2)

Fast Length Adjustment of SHort reads

flexbar (1:3.5.0-5)

flexible barcode and adapter removal for sequencing platforms

flextra (5.0-17)

Trajectory model for tracing air transport phenomena

flye (2.9.3+dfsg2-1)

de novo assembler for single molecule sequencing reads using repeat graphs

fml-asm (0.1+git20190320.b499514-1build1)

tool for assembling Illumina short reads in small regions

foma (1:0.10.0+s311-1.2build2)

Tools for constructing various finite-state automata

foma-bin (1:0.10.0+s311-1.2build2)

Transitional package for foma

form (4.3.0+git20230104+ds-1build2)

Symbolic manipulation system

fractalnow (0.8.2-5build2)

Fast, advanced fractal generator

free42-nologo (3.1.4+ds-1build2)

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

freebayes (1.3.7-1)

Bayesian haplotype-based polymorphism discovery and genotyping

freecad (0.21.2+dfsg1-6trisquel1)

Extensible Open Source CAx program

freecad-common (0.21.2+dfsg1-6trisquel1)

Extensible Open Source CAx program - common files

freecad-python3 (0.21.2+dfsg1-6trisquel1)

Extensible Open Source CAx program - Python 3 binaries

freecontact (1.0.21-13.1build2)

fast protein contact predictor

freesasa (2.1.2-4)

Solvent Accessible Surface Area of biomolecules

frog (0.20-2.1build1)

tagger and parser for natural languages (runtime)

frogdata (0.18-2)

Data files for Frog

fsa (1.15.9+dfsg-6)

Fast Statistical Alignment of protein, RNA or DNA sequences

fsm-lite (1.0-8)

frequency-based string mining (lite)

ftools-fv (5.5.2+dfsg-3)

Tool for viewing and editing FITS format files

ftools-pow (5.5.2+dfsg-3)

Curve plotting and image display interface tool

funtools (1.4.8-1.1build2)

Minimal buy-in FITS utility package

fxt-tools (0.3.13-4.1build1)

Multithreaded tracing library

gabedit (2.5.1+ds-1build3 [amd64, arm64, ppc64el, riscv64], 2.5.1+ds-1build2 [armhf])

graphical user interface to Ab Initio packages

galileo (0.5.1-9.1)

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

galileo-daemon (0.5.1-9.1)

Utility to securely synchronize a Fitbit device - daemon

gamgi (0.17.5-1build2)

General Atomistic Modelling Graphic Interface (GAMGI)

gamgi-data (0.17.5-1build2)

General Atomistic Modelling Graphic Interface (data)

garli (2.1-7build2)

phylogenetic analysis of molecular sequence data using maximum-likelihood

garli-examples (2.1-7build2)

phylogenetic analysis of molecular sequence data (examples)

garli-mpi (2.1-7build2)

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

garlic (1.6-3)

visualization program for biomolecules

gasic (0.0.r19-8)

genome abundance similarity correction

gasic-examples (0.0.r19-8)

genome abundance similarity correction (example data)

gatb-core (1.4.2+dfsg-13build2)

Genome Analysis Toolbox with de-Bruijn graph

gatb-core-testdata (1.4.2+dfsg-13build2)

Genome Analysis Toolbox with de-Bruijn graph (test data)

gausssum (3.0.2-2)

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

gbrowse (2.56+dfsg-12build3)

GMOD Generic Genome Browser

gbrowse-calign (2.56+dfsg-12build3)

CAlign helper

gbrowse-data (2.56+dfsg-12build3)

Sample data to use GBrowse

gbutils (6.3-1)

utilities for command line econometrics

gchempaint (0.14.17-6.2build2)

2D chemical structures editor for the GNOME2 desktop

gcrystal (0.14.17-6.2build2)

lightweight crystal structures visualizer

gcu-bin (0.14.17-6.2build2)

GNOME chemistry utils (helper applications)

gdal-bin (3.8.4+dfsg-3ubuntu3)

Geospatial Data Abstraction Library - Utility programs

gdal-data (3.8.4+dfsg-3ubuntu3)

Geospatial Data Abstraction Library - Data files

gdal-plugins (3.8.4+dfsg-3ubuntu3)

Geospatial Data Abstraction Library - Plugins

gdis (0.90-6build3 [amd64, arm64, ppc64el, riscv64], 0.90-6build2 [armhf])

molecular and crystal model viewer

gdis-data (0.90-6build3)

molecular and crystal model viewer (data files)

gdl-astrolib (2022.09.12+dfsg-1)

Low-level astronomy software for GDL

gdl-coyote (2022.04.12-1)

GDL library from D. Fannings IDL courses

gdl-mpfit (1.85+2017.01.03-4)

Robust non-linear least squares curve fitting for GDL

gdpc (2.2.5-16build2)

visualiser of molecular dynamic simulations

gdpc-examples (2.2.5-16build2)

example files for the gdpc program

gelemental (2.0.2-1.1build2)

Periodic Table viewer

gemma (0.98.5+dfsg-2)

Genome-wide Efficient Mixed Model Association

gemmi (0.6.4+ds-1build1)

library for structural biology - executable

genometester (4.0+git20200511.91cecb5+dfsg-1)

toolkit for performing set operations on k-mer lists

genomethreader (1.7.3+dfsg-10build2)

software tool to compute gene structure predictions

genometools (1.6.5+ds-2.1ubuntu2)

versatile genome analysis toolkit

genometools-common (1.6.5+ds-2.1ubuntu2)

shared data files for GenomeTools

genomicsdb-tools (1.5.0-2)

sparse array storage library for genomics (tools)

geographiclib-tools (2.3-1build1)

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

geotiff-bin (1.7.1-5build1)

GeoTIFF (geografic enabled TIFF) library -- tools

getdata (0.2-4)

management of external databases

gff2aplot (2.0-15)

pair-wise alignment-plots for genomic sequences in PostScript

gff2ps (0.98l-6)

produces PostScript graphical output from GFF-files

gffread (0.12.7-4build1)

GFF/GTF format conversions, region filtering, FASTA sequence extraction

gfsview-batch (20121130+dfsg-8.1build2)

batch-version of viewer for Gerris simulation files

gftl-dev (1.3.0+is-really-1.2.7-1)

Containers and iterators for Fortran

gftl-shared-dev (1.0.7-2)

Common gFTL containers of Fortran intrinsic types

ggd-utils (1.0.0+ds-1build1)

programs for use in ggd

ghmm (0.9~rc3-5.1ubuntu4)

General Hidden-Markov-Model library - tools

ginga (5.0.0-1)

Astronomical image viewer

gjh-asl-json (0.0+git20210628.867c5da-1)

gjh solver, like solver from AMPL Library

glam2 (1064-9)

gapped protein motifs from unaligned sequences

glgrib-data (1.0-3build8)

Display GRIB2 fields using OpenGL (data for glgrib)

glgrib-egl (1.0-3build8)

Render geophysical fields encoded in GRIB edition 2 using OpenGL

glgrib-glfw (1.0-3build8)

Interactive display for geophysical fields encoded in GRIB2

glgrib-shaders (1.0-3build8)

Display GRIB2 fields using OpenGL (shaders for glgrib)

glgrib-testdata (1.0-3build8)

Display GRIB2 fields using OpenGL (test data for glgrib)

glgrib-tk (1.0-3build8)

Display GRIB2 fields using OpenGL (Perl/Tk interface)

glueviz (1.17.1+dfsg-1)

Linked data visualization

gmap (2024-02-22+ds-1build1)

spliced and SNP-tolerant alignment for mRNA and short reads

gmt (6.5.0+dfsg-3build2)

Generic Mapping Tools

gmt-common (6.5.0+dfsg-3build2)

Generic Mapping Tools - Architecture-independent files

gmt-dcw (2.1.2-1)

Digital Chart of the World (DCW) for GMT

gmt-gshhg (2.3.7-6)

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

gmt-gshhg-full (2.3.7-6)

Full resolution coastlines for the Generic Mapping Tools

gmt-gshhg-high (2.3.7-6)

High resolution coastlines for the Generic Mapping Tools

gmt-gshhg-low (2.3.7-6)

Low resolution coastlines for the Generic Mapping Tools

gnuastro (0.22-3.1build2)

GNU Astronomy Utilities programs

goby-java (3.3.1+dfsg2-10)

next-generation sequencing data and results analysis tool

golang-github-brentp-gsort-dev (0.1.4-3build1)

library package for gsort

golang-github-gogetdata-ggd-utils-dev (1.0.0+ds-1build1)

library for use in ggd

gpaw (24.1.0-1build1)

DFT and beyond within the projector-augmented wave method

gpaw-data (24.1.0-1)

gpaw datasets/setups

gperiodic (3.0.3-1build2)

periodic table application

gpx (2.6.8-1)

Gcode to x3g conversion post processor

grabix (0.1.7-4)

wee tool for random access into BGZF files

grads (3:2.2.1-6build2)

Grid Analysis and Display System for earth science data

graphlan (1.1.3-4)

circular representations of taxonomic and phylogenetic trees

grass (8.3.2-1ubuntu2)

Geographic Resources Analysis Support System (GRASS GIS)

grass-core (8.3.2-1ubuntu2)

GRASS GIS core components

grass-doc (8.3.2-1ubuntu2)

GRASS GIS user documentation

grass-gui (8.3.2-1ubuntu2)

GRASS GIS graphical user interfaces

gravit (0.5.1+dfsg-6build2)

visually stunning gravity simulator

gravit-data (0.5.1+dfsg-6build2)

data files for Gravit

gri (2.12.27-1.1build2)

a language for scientific illustration

grinder (0.5.4-6)

Versatile omics shotgun and amplicon sequencing read simulator

gromacs (2023.3-1ubuntu3)

Molecular dynamics simulator, with building and analysis tools

gromacs-data (2023.3-1ubuntu3)

GROMACS molecular dynamics sim, data and documentation

gsort (0.1.4-3build1)

sort genomic data

gubbins (3.3.3-1)

phylogenetic analysis of genome sequences

gvb (1.4-1.1)

visual simulator of 1 and 2-dimensional vibrations

gwama (2.2.2+dfsg-5)

Genome-Wide Association Meta Analysis

gwyddion (2.64-1.1build3)

Scanning Probe Microscopy visualization and analysis tool

gwyddion-common (2.64-1.1build3)

architecture-independent files for Gwyddion SPM analysis tool

gyoto (2.0.2-1.1build3)

General relativistic geodesic integration and ray-tracing

gyoto-bin (2.0.2-1.1build3)

General relativistic ray-tracing command-line interface

h5utils (1.13.2-1build3)

HDF5 files visualization tools

harminv (1.4.2-1build1)

extraction of complex frequencies and amplitudes from time series

harvest-tools (1.3-8build5)

archiving and postprocessing for reference-compressed genomic multi-alignments

hdf-compass (0.7~b8-3)

viewer for HDF5 and related formats

hdf5-filter-plugin (0.0~git20221111.49e3b65-4build2)

external filters for HDF5: LZ4, BZip2, Bitshuffle

hdf5-filter-plugin-blosc-serial (0.0~git20220616.9683f7d-5build2)

blocking, shuffling and lossless compression library

hdf5-filter-plugin-zfp-serial (1.1.1-2build2)

Compression plugin for the HDF5 library using ZFP compression

hdf5-helpers (1.10.10+repack-3.1ubuntu4)

HDF5 - Helper tools

hdf5-tools (1.10.10+repack-3.1ubuntu4)

HDF5 - Runtime tools

herisvm (0.9.0-2)

machine learning tools for classification algorithms

hfst (3.16.0-5build4)

Helsinki Finite-State Transducer Technology

hfst-ospell (0.5.4-1build3)

Spell checker library and tool based on HFST

hhsuite (3.3.0+ds-8)

sensitive protein sequence searching based on HMM-HMM alignment

hhsuite-data (3.3.0+ds-8)

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

hilive (2.0a-3build4)

realtime alignment of Illumina reads

hinge (0.5.0-7build1)

long read genome assembler based on hinging

hisat2 (2.2.1-4)

graph-based alignment of short nucleotide reads to many genomes

hmmer (3.4+dfsg-2)

profile hidden Markov models for protein sequence analysis

hmmer2 (2.3.2+dfsg-12)

profile hidden Markov models for protein sequence analysis

hodie (1.5.0-4)

prints the date in Latin

hpcc (1.5.0-3build2)

HPC Challenge benchmark

htcondor (23.4.0+dfsg-1ubuntu4)

transitional dummy package

htcondor-annex-ec2 (23.4.0+dfsg-1ubuntu4)

transitional dummy package

htcondor-dev (23.4.0+dfsg-1ubuntu4)

transitional dummy package

htcondor-doc (23.4.0+dfsg-1ubuntu4)

transitional dummy package

htcondor-test (23.4.0+dfsg-1ubuntu4)

transitional dummy package

htcondor-upgrade-checks (23.4.0+dfsg-1ubuntu4)

transitional dummy package

hts-nim-tools (0.2.1-1)

tools biological sequences: bam-filter, count-reads, vcf-check

hyphy-common (2.5.59+dfsg-1build3)

Hypothesis testing using Phylogenies (common files)

hyphy-mpi (2.5.59+dfsg-1build3)

Hypothesis testing using Phylogenies (MPI version)

hyphy-pt (2.5.59+dfsg-1build3)

Hypothesis testing using Phylogenies (pthreads version)

idba (1.1.3-8)

iterative De Bruijn Graph short read assemblers

idba-extra (1.1.3-8)

iterative De Bruijn Graph short read assemblers (extra tools)

idseq-bench (0.0~git20210602.27fb6dc-1)

Benchmark generator for the IDseq Portal

igblast (1.19.0-1build1)

Immunoglobulin and T cell receptor variable domain sequence analysis

igdiscover (0.11-4)

analyzes antibody repertoires to find new V genes

ignition-common-cli (4.7.0+ds2-2.1build1)

Collection of useful code used by robotics apps - CLI tools

ignition-transport-cli (11.0.0+ds-4build4)

Ignition Robotics transport Library - CLI tools

igor (1.4.0+dfsg-4)

infers V(D)J recombination processes from sequencing data

igv (2.17.3+dfsg-1)

Integrative Genomics Viewer

iitii (0.0+git20191030.85209e0-2)

Implicit Interval Tree with Interpolation Index

illustrate (0.0+git20200923.217db48-2)

cartoonish representations of large biological molecules

imagej (1.54g-1)

Image processing program with a focus on microscopy images

imview (1.1.9h-4build3)

Image viewing and analysis application

indelible (1.03-6)

powerful and flexible simulator of biological evolution

indi-aagcloudwatcher-ng (1.7+20230106180155-1)

INDI driver for the AAG Cloud Watcher

indi-aok (2.0+20221222093242-1build1)

INDI driver for AOK Skywalker

indi-apogee (1.9+20221223184417-2)

INDI driver for Apogee CCDs and Filter Wheels

indi-armadillo-platypus (1.0+20221226082641-2)

INDI driver for Lunatico Astronomia Armadillo and Platypus

indi-astrolink4 (0.1+20221223182627-1)

INDI driver for Astrolink 4.0 devices

indi-astromechfoc (0.2+20221223181816-1)

INDI driver for Astromechanics Canon Lens Controller

indi-avalon (1.12+20221223132122-1)

INDI driver for Avalon Instruments mounts

indi-beefocus (0.1+20221222010828-1)

INDI driver for Bee Focus

indi-bresserexos2 (1.0+20221223130124-1build1)

INDI driver for Exos II GoTo Telescope Mount

indi-dreamfocuser (2.1+20221223125100-1)

INDI driver for DeamFocuser focuser

indi-dsi (0.4+20221223123028-1)

INDI driver for Meade DSI Pro I/II/III

indi-eqmod (1.0+20230126190232-1build1)

INDI EQMod Driver

indi-ffmv (0.3+20221223120905-2)

INDI driver for Point Grey Firefly MV cameras

indi-fli (1.5+20221225141318-1build2)

INDI driver for FLI CCD & Focuser

indi-gige (0.1+20221223115700-2build1)

INDI driver for GigE machine vision cameras

indi-gphoto (3.2+20221221172841-2build2)

INDI driver for GPhoto (DSLR) Cameras

indi-gpsd (0.5+20221222000619-1build3)

INDI driver for gpsd GPS daemon

indi-gpsnmea (0.2+20221223114018-1)

INDI driver for GPS NMEA streams

indi-limesdr (1.4+20221223110308-1build1)

INDI driver for LimeSDR (LMS7) Receiver

indi-maxdomeii (1.3+20221223105522-1)

INDI driver for MaxDome II dome control system

indi-mgen (0.1+20221222184336-1)

INDI driver for Lacerta MGen Autoguider

indi-nexdome (1.5+20221222183051-1)

INDI driver for NexDome

indi-nightscape (1.0.6+20221222181314-2)

INDI driver for Celestron Nightscape 8300

indi-orion-ssg3 (0.1+20221222180647-2)

INDI Driver for Orion StarShoot G3 and G4 cameras

indi-rtklib (1.0+20221222172722-1)

INDI driver for precise positioning with RTKLIB

indi-shelyak (1.0+20221222171819-1)

INDI driver for Shelyak and Alpy Spectrograph

indi-spectracyber (1.3+20221222164952-1build1)

INDI driver for hydrogen line spectrometer

indi-starbook (0.8+20221222163625-1build2)

INDI driver for Vixen Starbook telescope controllers

indi-starbook-ten (0.1-2build1)

INDI driver for Vixen Starbook Ten telescope controllers

indi-sx (1.16+20221222162728-2)

INDI driver for Starlight Xpress CCD and Filter Wheel

indi-talon6 (2.0+20221222160901-1)

INDI driver for Talon6 Roll Off Roof

indi-webcam (1.0+20221222161740-1build1)

INDI Driver for web cameras

indi-weewx-json (1.0-1build2)

INDI driver for the WeeWX Weather Station

indigo-utils (1.2.3-3.1build1)

Organic Chemistry Toolkit Utilities

infernal (1.1.5-2)

inference of RNA secondary structural alignments

inhomog (0.1.9.2-1build3)

kinematical backreaction and average scale factor evolution

inkscape-speleo (1.8-4)

Inkscape plugin to help draw surveys

inkscape-survex-export (2.0-1)

Inkscape plugin to digitise printed surveys

insilicoseq (2.0.0-1)

sequencing simulator producing realistic Illumina reads

ipig (0.0.r5-4)

integrating PSMs into genome browser visualisations

iqtree (2.0.7+dfsg-1build2)

efficient phylogenetic software by maximum likelihood

iraf (2.17.1-5build3)

Image Reduction and Analysis Facility

iraf-dev (2.17.1-5build3)

Image Reduction and Analysis Facility (development files)

iraf-fitsutil (2018.07.06-7ubuntu1)

FITS utilities for IRAF

iraf-mscred (5.05+2018.07.09-3build2)

CCD mosaic reduction package for IRAF

iraf-noao (2.17.1-5build3)

IRAF NOAO data reduction package

iraf-noao-dev (2.17.1-5build3)

IRAF NOAO data reduction package (development files)

iraf-rvsao (2.8.5-2build2)

IRAF package to obtain radial velocities from spectra

iraf-sptable (1.0~pre20180612-3build2)

IRAF package for Tabular Spectra

iraf-st4gem (1.0+ds-2build2)

Selected tools from the Space Telescope Science Data Analysis System

iraf-wcstools (3.9.7-1.1build1)

Handle the WCS of a FITS image (IRAF package)

iraf-xdimsum (2003.01.24-2)

Deep Infrared Mosaicing Software

ismrmrd-schema (1.8.0-2build5)

schema for ISMRMRD

ismrmrd-tools (1.8.0-2build5)

command-line tools for ISMRMRD

iva (1.0.11+ds-5)

iterative virus sequence assembler

ivar (1.4.2+dfsg-2ubuntu2)

functions broadly useful for viral amplicon-based sequencing

jaligner (1.0+dfsg-11)

Smith-Waterman algorithm with Gotoh's improvement

jalview (2.11.3.1+dfsg-1)

multiple alignment editor

jblas (1.2.5+dfsg-1)

fast linear algebra library for Java

jbmc (5.95.1-4ubuntu1)

bounded model checker for Java programs

jellyfish (2.3.1-3build1)

count k-mers in DNA sequences

jellyfish-examples (2.3.1-3build1)

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

jellyfish1 (1.1.11-9)

count k-mers in DNA sequences

jemboss (6.6.0+dfsg-12ubuntu2)

graphical user interface to EMBOSS

jmodeltest (2.1.10+dfsg-12)

HPC selection of models of nucleotide substitution

jmol (14.32.83+dfsg-3)

Molecular Viewer

jsamp (1.3.7-1)

Java Simple Application Messaging Protocol tool for VO

jube (2.5.1-1)

JUBE Benchmarking Environment

jupyter-notebook (6.4.12-2.2ubuntu1)

Jupyter interactive notebook

kalign (1:3.3.5-1)

Global and progressive multiple sequence alignment

kallisto (0.48.0+dfsg-4build1)

near-optimal RNA-Seq quantification

kallisto-examples (0.48.0+dfsg-4build1)

near-optimal RNA-Seq quantification (example data)

kalzium (4:23.08.5-0ubuntu4)

periodic table and chemistry tools

kalzium-data (4:23.08.5-0ubuntu4)

data files for Kalzium

kaptive (2.0.8-1)

obtain information about K and O types for Klebsiella genome assemblies

kaptive-data (2.0.8-1)

reference data for kaptive for Klebsiella genome assemblies

kaptive-example (2.0.8-1)

example data for kaptive for Klebsiella genome assemblies

khmer-common (3.0.0~a3+dfsg-8build1)

common files for the khmer project tools

kineticstools (0.6.1+git20220223.1326a4d+dfsg-2build2)

detection of DNA modifications

kineticstools-data (0.6.1+git20220223.1326a4d+dfsg-2build2)

detection of DNA modifications -- data files

king-probe (02.21-1)

Evaluate and visualize protein interatomic packing

kissplice (2.6.2-2)

Detection of various kinds of polymorphisms in RNA-seq data

kleborate (2.4.1-3build1)

tool to screen Klebsiella genome assemblies

kleborate-examples (2.4.1-3build1)

tool to screen Klebsiella genome assemblies (example data)

klustakwik (3.0.2+ds-2)

automatic sorting of the samples (spikes) into clusters

kma (1.4.14-2)

mapping genomic sequences to raw reads directly against redundant databases

kmc (3.2.4+dfsg-1)

count kmers in genomic sequences

kmer (0~20150903+r2013-8build4)

suite of tools for DNA sequence analysis

kmer-examples (0~20150903+r2013-8build4)

sample data for kmer suite of tools for DNA sequence analysis

kmerresistance (2.2.0-4ubuntu1)

correlates mapped genes with the predicted species of WGS samples

kokkos (3.7.01-2.1build1)

C++ Performance Portability Programming

konclude (0.7.0+1138+git20220514~dfsg-1build3)

tableau-based description logic reasoner for the semantic web

kraken (1.1.1-4)

assigning taxonomic labels to short DNA sequences

kraken2 (2.1.3-1)

taxonomic classification system using exact k-mer matches

kst (2.0.8-5build4)

scientific data plotting tool

kstars (5:3.6.2-2ubuntu5)

desktop planetarium, observation planning and telescope control

kstars-data (5:3.6.2-2ubuntu5)

data files for KStars desktop planetarium

kstars-data-extra-tycho2 (1.1r1-9.1build1)

Tycho-2 star catalog for KStars

lagan (2.0-10)

highly parametrizable pairwise global genome sequence aligner

lamarc (2.1.10.1+dfsg-7build3)

Likelihood Analysis with Metropolis Algorithm using Random Coalescence

lambda-align (1.0.3-6)

Local Aligner for Massive Biological DatA

lambda-align2 (2.0.1-1)

Local Aligner for Massive Biological DatA - v2

lammps (20240207+dfsg-1.1build3)

Molecular Dynamics Simulator

last-align (1542-1)

genome-scale comparison of biological sequences

lastz (1.04.22-2)

pairwise aligning DNA sequences

lastz-examples (1.04.22-2)

pairwise aligning DNA sequences (examples and test scripts)

leaff (0~20150903+r2013-8build4)

biological sequence library utilities and applications

lefse (1.1.2-1)

determine features of organisms, clades, taxonomic units, genes

lexd (1.3.1-1build2)

Lexicon compiler for non-suffixational morphologies

libadios-bin (1.13.1-36)

ADIOS Adaptable IO system for simulations - binaries

libadios-examples (1.13.1-36)

Examples for the ADIOS Adaptable IO system

libatlas-ecmwf-utils (0.36.0-2)

Numerical weather prediction and climate modelling library - utilities

libball1.5-data (1.5.0+git20180813.37fc53c-11build5)

Biochemical Algorithms Library (data files)

libbio-db-hts-perl (3.01-4build3)

Perl interface to the HTS library

libbio-tools-phylo-paml-perl (1.7.3-4)

Bioperl interface to the PAML suite

libbio-tools-run-alignment-clustalw-perl (1.7.4-3)

Bioperl interface to Clustal W

libbio-tools-run-alignment-tcoffee-perl (1.7.4-3)

Bioperl interface to T-Coffee

libbiojava-java (1:1.9.7+dfsg-1)

Java API to biological data and applications (default version)

libca4.14.2 (7.0.7+dfsg1-5)

EPICS channel access client library

libcassie1v5 (1.0.9-4build3)

library implementating search algorithms

libcg3-1 (1.4.6-1build2)

Runtime for CG-3

libchemicaltagger-java (1.6.2-2)

tool for semantic text-mining in chemistry

libclhep2.1t64 (2.1.4.1+dfsg-1.2build1)

CLHEP: A Class Library for High Energy Physics

libcom3.22.0 (7.0.7+dfsg1-5)

EPICS common library

libdbcsr-dev (2.6.0-2)

Distributed Block Compressed Sparse Row matrix library

libdivsufsort3 (2.0.1-6)

fast suffix array construction

libdlpack-dev (0.6-1)

Open In Memory Tensor Structure

libdyssol1.0t64 (1.1.1+ds1-2.1build4)

Tool for dynamic flowsheet simulation. Shared libraries

libeccodes-data (2.34.1-1build2)

GRIB and BUFR enecoding/encoding software library - data

libeckit-utils (1.25.2-2build4)

C++ toolkit for ECMWF tools and applications - development files

libej0 (5.3.1+repack-6build1)

hardware & software framework for developing science experiments

libfckit-utils (0.12.0-1build1)

Library Fortran toolkit for interoperating Fortran with C/C++

libgenometools0 (1.6.5+ds-2)

versatile genome analysis library

libgfsgl0t64 (20121130+dfsg-8.1build2)

graphical viewer for Gerris simulation files. Shared library

libghemical-data (3.0.0-4.4build2)

Molecular Modelling Library (data files)

libgiac0 (1.9.0.69+dfsg2-1)

Computer Algebra System C++ library

libgoby-io-java (3.3.1+dfsg2-10)

IO API for goby

libhdf5-jni (1.10.10+repack-3.1ubuntu4)

native library used by libhdf5-java

libideep-dev (0.0~git20230825.6f4d653-2)

Intel's mkldnn/dnnl wrapper for pytorch

libinchi-bin (1.03+dfsg-4build1)

International Chemical Identifier (InChI) algorithm (executable)

libjgrapht-java (1.5.2-1)

Java library of graph theory data structures and algorithms

libjgrapht-java

virtual package provided by libjgrapht0.8-java

liblammps-dev (20240207+dfsg-1.1build3)

Molecular Dynamics Simulator (dev files)

liblammps0t64 (20240207+dfsg-1.1build3)

Molecular Dynamics Simulator (shared library)

liblemon-utils (1.3.1+dfsg-6build1)

Library for Efficient Modeling and Optimization in Networks (utilities)

libliggghts3t64 (3.8.0+repack1-9.1build2)

Open Source DEM Particle Simulation Software. Shared library

liblinear-tools (2.3.0+dfsg-5build1)

Standalone applications for LIBLINEAR

liblorene-debian1t64 (0.0.0~cvs20161116+dfsg-1.3build1)

liblorene shared library

liblorene-export-debian0t64 (0.0.0~cvs20161116+dfsg-1.3build1)

liblorene_export shared library

liblorenef77-debian1t64 (0.0.0~cvs20161116+dfsg-1.3build1)

liblorenef77 shared library

libmcpl-dev (1.3.2-3.1build1)

Monte Carlo Particle Lists - development files

libmcpl1 (1.3.2-3.1build1)

Monte Carlo Particle Lists - library

libmstoolkit-tools (82-7.1build2)

libraries for manipulating mass spectrometry data - tools

libncarg-bin (6.6.2.dfsg.1-4)

NCAR command-language library - development tools

libncarg-data (6.6.2.dfsg.1-4)

NCAR command-language library - Data

libocas-tools (0.97+dfsg-8build1)

Standalone applications implementing the OCAS solver

libonnx-dev (1.14.1-2.1build2)

Open Neural Network Exchange (ONNX) (dev)

libonnx-testdata (1.14.1-2.1build2)

Open Neural Network Exchange (ONNX) (test data)

libonnx1t64 (1.14.1-2.1build2)

Open Neural Network Exchange (ONNX) (libs)

libopenfoam (1912.200626-2build3)

Open source toolbox for Computational Fluid Dynamics (CFD) - libraries

liboscar4-java (5.2.0+dfsg-2)

automated annotation of chemistry in scientific articles

libphitsmcpl1 (1.3.2-3.1build1)

Monte Carlo Particle Lists - PHITS library

libpluto-jpl-eph-dev (0.0~git20180228-1.1build1)

development files to interact with JPL ephemeres data

libpluto-lunar-dev (0.0~git20180825.e34c1d1-1build1)

development files for astronomical Lunar library

libpwiz-tools (3.0.18342-4.1build3)

ProteoWizard command line tools

libqgis-customwidgets (3.34.4+dfsg-4build2)

QGIS custom widgets for Qt Designer

librasterlite2-1 (1.1.0~beta1-3build5)

library for huge raster coverages using a SpatiaLite DBMS

librsl1 (1.43-1.2build1)

TRMM Radar Software Library

libsigmf (1.0.2-2)

SigMF data format handling library

libsilo-bin (4.11-5)

Utilities to manipulate libsilo files

libsmiles-scripts-java (0.2.0+dfsg1-5)

command line tools to handle SMILES descriptors - Java libraries

libsmiles-scripts-perl (0.2.0+dfsg1-5)

command line tools to handle SMILES descriptors - Perl libraries

libsqlite3-mod-virtualpg (2.0.1-4build1)

Loadable dynamic extension to both SQLite and SpatiaLite

libsquizz (0.99d+dfsg-3)

Conversion libs used by squizz genetic sequence converter

libssm-bin (1.4.0-2build1)

macromolecular superposition library - binaries

libsswmcpl1 (1.3.2-3.1build1)

Monte Carlo Particle Lists - SSW library

libstxxl1t64 (1.4.1-4.1build1)

C++ Standard Template Library for extra large datasets

libtrexio0 (2.2.3-3build2)

TREX I/O library for efficient data I/O in quantum chemistry.

libuhd4.6.0-dpdk-tests (4.6.0.0+ds1-5.1build4)

universal hardware driver for Ettus Research products - DPDK tests

libvcflib-tools (1.0.9+dfsg1-3build1)

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

libxgboost-predictor-java (0.3.1+dfsg-2)

Java implementation of XGBoost predictor for online prediction tasks

libxy-bin (1.6-3.1build1)

xylib - utilities

liggghts (3.8.0+repack1-9.1build2)

Open Source DEM Particle Simulation Software.

lighter (1.1.2-7)

fast and memory-efficient sequencing error corrector

litl-tools (0.1.9-13)

Lightweight Trace Library - tools

loki (2.4.7.4-10)

MCMC linkage analysis on general pedigrees

loki-doc (2.4.7.4-10)

MCMC linkage analysis on general pedigrees (PS manual)

looktxt (1.4.1-3)

Convert free format text file into scientific data formats

looptools (2.16-1)

Integral Evaluator of One-loop Feynman Diagram

lorene (0.0.0~cvs20161116+dfsg-1.3build1)

framework for numerical relativity

lorene-codes-src (0.0.0~cvs20161116+dfsg-1.3build1)

source files of LORENE-based codes

ltrsift (1.0.2-9ubuntu2)

postprocessing and classification of LTR retrotransposons

lttoolbox-dev (3.7.6-1build1)

Development tools and library for lttoolbox

lucy (1.20-4)

DNA sequence quality and vector trimming tool

lumpy-sv (0.3.1+dfsg-7build3)

general probabilistic framework for structural variant discovery

lumpy-sv-examples (0.3.1+dfsg-7build3)

general probabilistic framework for structural variant discovery (data)

lutefisk (1.0.7+dfsg-7)

de novo interpretation of peptide CID spectra

lxi-tools (2.7-1build2)

LAN eXtensions for Instrumentation (LXI) software interface

macs (3.0.1-2build1)

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

macsyfinder (2.1.3-1build1)

detection of macromolecular systems in protein datasets

maffilter (1.3.1+dfsg-5build3)

process genome alignment in the Multiple Alignment Format

maffilter-examples (1.3.1+dfsg-5build3)

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

mafft (7.505-1)

Multiple alignment program for amino acid or nucleotide sequences

malt (0.5.2-3)

sequence alignment and analysis tool to process sequencing data

mandelbrot-solver (3.2.1-10.1build4)

Solver for Mandelbrot polynomials based on MPSolve

mapdamage (2.2.1+dfsg-3)

tracking and quantifying damage patterns in ancient DNA sequences

mapsembler2 (2.2.4+dfsg1-4)

bioinformatics targeted assembly software

maq (0.7.1-9)

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

maqview (0.2.5-11)

graphical read alignment viewer for short gene sequences

mash (2.3+dfsg-6)

fast genome and metagenome distance estimation using MinHash

massxpert (8.3.0-1build2)

transitional package for massxpert -> massxpert2

massxpert-data (7.0.0-2)

polymer chemistry modelling and mass spectrometry data simulation (data)

massxpert2 (8.3.0-1build2)

polymer chemistry modelling and mass spectrometry data simulation (runtime)

massxpert2-data (8.3.0-1build2)

polymer chemistry modelling and mass spectrometry data simulation (data)

maude (3.2-2build1 [amd64, arm64, ppc64el, riscv64], 3.2-2 [armhf])

high-performance logical framework

mauve-aligner (2.4.0+4736-6)

multiple genome alignment

mayavi2 (4.8.1-3build1)

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

mbpoll (1.4.11+dfsg-2build1)

command line utility to communicate with ModBus slave (RTU or TCP)

mbt (3.6-3.1build2)

memory-based tagger-generator and tagger

mbtserver (0.14-2.1build1)

Server extensions for the MBT tagger

mcaller (1.0.3+git20210624.b415090-3)

find methylation in nanopore reads

mcpl (1.3.2-3.1build1)

Monte Carlo Particle Lists - libraries and tools

mecat2 (0.0+git20200428.f54c542+ds-4)

ultra-fast and accurate de novo assembly tools for SMRT reads

meep (1.25.0-2)

software package for FDTD simulation

meep-mpi-default (1.25.0-2)

software package for FDTD simulation, parallel (OpenMPI) version

meep-openmpi (1.25.0-2)

software package for FDTD simulation, parallel (OpenMPI) version

megadepth (1.2.0-4build2)

computes coverage from BigWig and BAM sequencing files

megahit (1.2.9-5)

ultra-fast and memory-efficient meta-genome assembler

megan-ce (6.21.1+dfsg-3)

interactive tool to explore and analyse microbiome sequencing data

melting (5.2.0-2)

compute the melting temperature of nucleic acid duplex

merkaartor (0.19.0+ds-5)

map editor for OpenStreetMap.org

meryl (0~20150903+r2013-8build4)

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

metabat (2.15-4)

robust statistical framework for reconstructing genomes from metagenomic data

metaeuk (6-a5d39d9+ds-4)

sensitive, high-throughput gene discovery and annotation for metagenomics

metaeuk-examples (6-a5d39d9+ds-4)

optional resources for the metaeuk package

metaphlan (4.0.4-1)

Metagenomic Phylogenetic Analysis

metaphlan2-data (2.6.0+ds-4)

data package for Metagenomic Phylogenetic Analysis

metastudent (2.0.1-9)

predictor of Gene Ontology terms from protein sequence

metastudent-data (2.0.1-8)

predictor of Gene Ontology terms from protein sequence - data files

metastudent-data-2 (1.0.0-6)

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

metview (5.21.2-1build3)

Interactive data visualization and analysis environment,

metview-data (5.21.2-1build3)

Data needed for the Metview data analysis environment

mhap (2.1.3+dfsg-3)

locality-sensitive hashing to detect long-read overlaps

mia-doctools (2.4.7-13build4)

Helper scripts for run-time document creation

mia-tools (2.4.7-13build4)

Command line tools for gray scale image processing

mialmpick (0.2.15-2build3)

Tools for landmark picking in 3D volume data sets

microbegps (1.0.0-6)

explorative taxonomic profiling tool for metagenomic data

microbiomeutil (20101212+dfsg1-6)

Microbiome Analysis Utilities

microbiomeutil-data (20101212+dfsg1-6)

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

microhope (5.3.1+repack-6build1)

hardware & software framework to learn microcontrollers

minc-tools (2.3.00+dfsg-10build2)

MNI medical image format tools

mindthegap (2.3.0-3build2)

performs detection and assembly of DNA insertion variants in NGS read datasets

mindthegap-examples (2.3.0-3build2)

optional scripts and example resources for mindthegap

minexpert2 (9.3.1-1)

MS^n mass spectrometric data visualization and mining (runtime)

minia (3.2.6-4build2)

short-read biological sequence assembler

miniasm (0.3+dfsg-4)

ultrafast de novo assembler for long noisy DNA sequencing reads

minicondor (23.4.0+dfsg-1ubuntu4)

distributed workload management system - single node configuration

minihtcondor (23.4.0+dfsg-1ubuntu4)

transitional dummy package

minimac4 (4.1.6-1)

Fast Imputation Based on State Space Reduction HMM

minimap (0.2-8)

tool for approximate mapping of long biosequences such as DNA reads

minimap2 (2.26+dfsg-1build1)

versatile pairwise aligner for genomic and spliced nucleotide sequences

minisat (1:2.2.1-8build1)

Fast and lightweight SAT solver

minisat+ (1.0-4build1)

solver for pseudo-Boolean constraints

mipe (1.1-9)

Tools to store PCR-derived data

mira-assembler (4.9.6-11)

Whole Genome Shotgun and EST Sequence Assembler

mira-rfam-12s-rrna (4.9.6-11)

extract of RFAM 12 rRNA database

mirtop (0.4.25-5)

annotate miRNAs with a standard mirna/isomir naming

missfits (2.8.0-5)

Basic maintenance and packaging tasks on FITS files

mitools (2.0.5-5build4)

view, convert and perform basic maths with medical image datasets

mlpack-bin (4.3.0-2build1)

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

mlv-smile (1.47-8)

Find statistically significant patterns in sequences

mmb (4.0.0+dfsg-3.1build1)

model the structure and dynamics of macromolecules

mmb-common (4.0.0+dfsg-3.1build1)

model the structure and dynamics of macromolecules (common files)

mmmulti (0.1-3)

memory backed multimap

mmseqs2 (15-6f452+ds-2)

ultra fast and sensitive protein search and clustering

mmseqs2-examples (15-6f452+ds-2)

optional resources for the mmseqs2 package

mocassin (2.02.73.2-1)

MOnte CArlo SimulationS of Ionised Nebulae

mocassin-benchmarks (2.02.73.2-1)

benchmarks for the photoionisation code MOCASSIN

mocassin-data (2.02.73.2-1)

atomic and optical data for the photoionisation code MOCASSIN

mocassin-examples (2.02.73.2-1)

Examples for the photoionisation code MOCASSIN

molequeue (0.9.0-1build3)

Desktop integration of high performance computing resources

montage (6.0+dfsg-9)

Toolkit for assembling FITS images into mosaics

montage-gridtools (6.0+dfsg-9)

Create files to run montage on the grid

mopac (22.0.6+dfsg-1)

Molecular Orbital PACkage (MOPAC)

mopac7-bin (1.15-6ubuntu4)

Semi-empirical Quantum Chemistry Library (binaries)

mosdepth (0.3.6+ds-1)

BAM/CRAM depth calculation biological sequencing

mosdepth-examples (0.3.6+ds-1)

Test data for mosdepth

mothur (1.48.0-2build2)

sequence analysis suite for research on microbiota

mpb (1.11.1-5ubuntu1)

MIT Photonic-Bands

mpb-mpi (1.11.1-5ubuntu1)

MIT Photonic-Bands, parallel (mpich) version

mpb-scm (1.11.1-5ubuntu1)

MIT Photonic-Bands initialisation files

mpgrafic (0.3.19-1build3)

MPI version of N-body initial conditions grafic package

mpqc (2.3.1-22build2)

Massively Parallel Quantum Chemistry Program

mpqc-support (2.3.1-22build2)

Massively Parallel Quantum Chemistry Program (support tools)

mpsolve (3.2.1-10.1build4)

Multiprecision polynomial solver (command line version)

mptp (0.2.4-3build1)

single-locus species delimitation

mrbayes-mpi (3.2.7a-7build2)

Bayesian Inference of Phylogeny - mpi version

mricron (1.2.20211006+dfsg-5)

magnetic resonance image conversion, viewing and analysis

mricron-data (1.2.20211006+dfsg-5)

data files for MRIcron

mrpt-apps (1:2.12.0+ds-1.1build1)

Mobile Robot Programming Toolkit - Console and GUI applications

mrpt-common (1:2.12.0+ds-1.1build1)

Mobile Robot Programming Toolkit - Example datasets and files

mrtrix3 (3.0.4-1build2)

diffusion-weighted MRI white matter tractography

mseed2sac (2.3+ds1-1build1)

Convert MiniSEED time series data to SAC

multiqc (1.18+dfsg-1ubuntu1)

output integration for RNA sequencing across tools and samples

mummer (3.23+dfsg-8)

Efficient sequence alignment of full genomes

munipack (0.6.1-1build3)

Astronomical photometry software package

munipack-cli (0.6.1-1build3)

Command line interface of Munipack

munipack-core (0.6.1-1build3)

Core routines of Munipack

munipack-gui (0.6.1-1build3)

Graphical user interface of Munipack

murasaki (1.68.6-13build6)

homology detection tool across multiple large genomes

murasaki-common (1.68.6-13build6)

homology detection tool across multiple large genomes (common files)

murasaki-mpi (1.68.6-13build6)

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

muscle (1:5.1.0-1)

Multiple alignment program of protein sequences

muscle3 (3.8.1551-3)

multiple alignment program of protein sequences

music-bin (1.2.1-0.3build2)

Multi-Simulation Coordinator for MPI -- Utilities

mustang (3.2.4-1)

multiple structural alignment of proteins

mustang-testdata (3.2.4-1)

multiple structural alignment of proteins, test data

nanolyse (1.2.0-4)

remove lambda phage reads from a fastq file

nanook (1.33+dfsg-5)

pre- and post-alignment analysis of nanopore sequencing data

nanook-examples (1.33+dfsg-5)

pre- and post-alignment analysis of nanopore sequencing data (examples)

nanopolish (0.14.0-1ubuntu3)

consensus caller for nanopore sequencing data

nanostat (1.4.0-3)

statistics on long biological sequences

nanosv (1.2.4+git20190409.c1ae30c-6)

structural variant caller for nanopore data

nast-ier (20101212+dfsg1-6)

NAST-based DNA alignment tool

nautic (1.5-6build3)

computation of observer position in astro-navigation

ncbi-acc-download (0.2.8-1)

download genome files from NCBI by accession

ncbi-blast+ (2.12.0+ds-4build2)

next generation suite of BLAST sequence search tools

ncbi-blast+-legacy (2.12.0+ds-4build2)

NCBI Blast legacy call script

ncbi-cn3d (3.0.20170106+dfsg2-2)

3-dimensional viewer for biological molecules

ncbi-entrez-direct (19.2.20230331+dfsg-3)

NCBI Entrez utilities on the command line

ncbi-epcr (2.3.12-1-9)

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

ncbi-rrna-data (6.1.20170106+dfsg2-2)

large rRNA BLAST databases distributed with the NCBI toolkit

ncbi-seg (0.0.20000620-6)

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

ncbi-tools-bin (6.1.20170106+dfsg2-2)

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11 (6.1.20170106+dfsg2-2)

NCBI libraries for biology applications (X-based utilities)

ncl-ncarg (6.6.2.dfsg.1-4)

NCAR Command Language and NCAR graphics

ncl-tools (2.1.21+git20210811.b1213a7-5)

tools to deal with NEXUS files

ncoils (2002-9)

coiled coil secondary structure prediction

ncview (2.1.8+ds-5build3)

X11 visual browser for NetCDF format files

neat (2.3.2-2build3)

Nebular Empirical Analysis Tool

neobio (0.0.20030929-6)

computes alignments of amino acid and nucleotide sequences

netcdf-bin (1:4.9.2-5ubuntu4)

Programs for reading and writing NetCDF files

neurodebian (0.42.1)

neuroscience-oriented distribution - repository configuration

neurodebian-archive-keyring (0.42.1)

neuroscience-oriented distribution - GnuPG archive keys

neurodebian-desktop (0.42.1)

neuroscience-oriented distribution - desktop integration

neurodebian-dev (0.42.1)

neuroscience-oriented distribution - development tools

neurodebian-freeze (0.42.1)

nd_freeze tool to freeze APT sources to use snapshots

neurodebian-popularity-contest (0.42.1)

neuroscience-oriented distribution - popcon integration

neuron (8.2.2-6build2)

Simulation environment for computational models of neurons

neuron-dev (8.2.2-6build2)

Neuron simulation environment - Development files

nexus-tools (4.4.3-6build3)

NeXus scientific data file format - applications

ngmlr (0.2.7+git20210816.a2a31fb+dfsg-2)

CoNvex Gap-cost alignMents for Long Reads

nim-kexpr-dev (0.0.2-3)

kexpr math expressions for nim

nim-lapper-dev (0.1.7-5)

simple, fast interval searches for nim

njplot (2.4-9build2)

phylogenetic tree drawing program

nmodl (0.6-2build2)

Code generation engine for the NEURON modeling language

norsnet (1.0.17-7)

tool to identify unstructured loops in proteins

norsp (1.0.6-7)

predictor of non-regular secondary structure

nrn-mod2c (0.9+git220919-2)

NMODL to C converter for CoreNEURON

ntcard (1.2.2+dfsg-8ubuntu2)

Streaming algorithm to estimate cardinality in genomics datasets

nthash (2.3.0+dfsg-1ubuntu1)

Methods to evaluate runtime and uniformity tests for hashing methods

numdiff (5.9.0-1)

Compare similar files with numeric fields

nutsqlite (2.0.6-4)

Dietary nutrition analysis software

nwchem (7.2.2-1build3)

High-performance computational chemistry software (default MPI)

nwchem-data (7.2.2-1build3)

High-performance computational chemistry software (data files)

nwchem-mpich (7.2.2-1build3)

High-performance computational chemistry software (MPICH build)

nwchem-openmpi (7.2.2-1build3)

High-performance computational chemistry software (OpenMPI build)

nxtrim (0.4.3+dfsg-3)

Optimized trimming of Illumina mate pair reads

oar-common (2.5.10-1)

OAR batch scheduler common package

oar-node (2.5.10-1)

OAR batch scheduler node package

oar-restful-api (2.5.10-1)

OAR web services

oar-server (2.5.10-1)

OAR batch scheduler server package

oar-server-mysql (2.5.10-1)

OAR batch scheduler MySQL server backend package

oar-server-pgsql (2.5.10-1)

OAR batch scheduler PostgreSQL server backend package

oar-user (2.5.10-1)

OAR batch scheduler user package

oar-user-mysql (2.5.10-1)

OAR batch scheduler MySQL user backend package

oar-user-pgsql (2.5.10-1)

OAR batch scheduler PostgreSQL user backend package

oar-web-status (2.5.10-1)

OAR batch scheduler visualization tool package

occt-draw (7.6.3+dfsg1-7.1build1)

Open CASCADE Technology command interpreter and graphical test system

octave-bart (0.9.00-2build2)

Octave bindings for BART

octave-biosig (2.6.0-1ubuntu1)

Octave bindings for BioSig library

octave-gdf (0.1.3-11.1build1)

IO library for the GDF -- Octave interface

octave-jsonlab (2.0-2)

native JSON/UBJSON/MassagePack encoder/decoder for Octave

octave-psychtoolbox-3 (3.0.19.5.dfsg1-1build3)

toolbox for vision research -- Octave bindings

octave-zmat (0.9.8+ds-8)

in-memory data compression for Octave

octomap-tools (1.9.7+dfsg-3.1build3)

Tools for 3D occupancy grid mapping

octovis (1.9.7+dfsg-3.1build3)

Visualization tool for OctoMap

odil (0.12.2-4.1build1)

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

odin (2.0.5-5build4)

develop, simulate and run magnetic resonance sequences

ogdi-bin (4.1.1+ds-3build1)

Open Geographic Datastore Interface Library -- utilities

ompl-demos (1.5.2+ds1-1.1build2)

Open Motion Planning Library (OMPL) demos

ompl-plannerarena (1.5.2+ds1-1.1build2)

Open Motion Planning Library (OMPL) plannerarena

ont-fast5-api (4.1.1+dfsg-3build2)

simple interface to HDF5 files of the Oxford Nanopore .fast5 file format

openbabel (3.1.1+dfsg-9ubuntu5)

Chemical toolbox utilities (cli)

openbabel-gui (3.1.1+dfsg-9ubuntu5)

Chemical toolbox utilities (graphical user interface)

opendrop (3.3.1-6build2)

fully-featured pendant drop tensiometry software

openfoam (1912.200626-2build3)

Open source toolbox for Computational Fluid Dynamics (CFD) - binaries

openfoam-examples (1912.200626-2build3)

Open source toolbox for Computational Fluid Dynamics (CFD) - examples

openmolcas (23.10-1build2)

Quantum chemistry software package

openmolcas-data (23.10-1build2)

Quantum chemistry software package (data files)

openms (2.6.0+cleaned1-4build4)

package for LC/MS data management and analysis

openms-common (2.6.0+cleaned1-4build4)

package for LC/MS data management and analysis - shared data

openrocket (15.03.6)

Model Rocket Simulator

openstructure (2.5.0-1ubuntu5)

Open-Source Computational Structural Biology Framework

openturns-common (1.21.1-4ubuntu5)

generic tool to treat and quantify uncertainties (common files)

openuniverse (1.0beta3.1+dfsg-7.1build1)

3D Universe Simulator

openuniverse-common (1.0beta3.1+dfsg-7.1build1)

3D Universe Simulator data files

optgeo (2.25-4)

simulator for geometrical optics

opticalraytracer (9.6-4)

Virtual lens/mirror design workshop

optimir (1.2-1)

Integrating genetic variations in miRNA alignment

orthanc (1.12.2+dfsg-1build4)

Lightweight, RESTful DICOM server for medical imaging

orthanc-dicomweb (1.16+dfsg-1build2)

Plugin to extend Orthanc with support of WADO and DICOMweb

orthanc-gdcm (1.6+dfsg-1build2)

DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)

orthanc-imagej (1.2+dfsg-4)

ImageJ plugin to import images from Orthanc

orthanc-mysql (5.0+dfsg-1build3)

Plugins to use MySQL or MariaDB as a database back-end to Orthanc

orthanc-neuro (1.0-2build4)

Neuroimaging plugin for Orthanc

orthanc-postgresql (5.0+dfsg-2build3)

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

orthanc-python (4.1+ds-2ubuntu2)

Develop plugins for Orthanc using the Python programming language

orthanc-webviewer (2.8-4build1)

Web viewer of medical images for Orthanc

orthanc-wsi (2.0+dfsg-2build5)

Whole-slide imaging support for Orthanc (digital pathology)

oscar (1.5.1-1build2)

Open Source CPAP Analysis Reporter (OSCAR)

osra (2.1.3-3build3)

optical structure recognition

otf-trace (1.12.5+dfsg-8build2)

Open Trace Format support library - development files

otf2-tools (3.0.3-3.1build1)

Open Trace Format support library - tools

packmol (1:20.14.3-1)

Initial configurations for Molecular Dynamics Simulations

paje.app (1.98-1.1build1)

generic visualization tool (Gantt chart and more)

pal2nal (14.1-3)

converts proteins to genomic DNA alignment

paleomix (1.3.8-1)

pipelines and tools for the processing of ancient and modern HTS data

paml (4.9j+dfsg-4)

Phylogenetic Analysis by Maximum Likelihood (PAML)

pan-config (0.4)

PAN Blend config package

pan-tasks (0.4)

PAN Blends tasks for tasksel

paraclu (10-1)

Parametric clustering of genomic and transcriptomic features

parafly (0.1.0-4)

parallel command processing using OpenMP

parallel-fastq-dump (0.6.7-3)

parallel fastq-dump wrapper

paraview (5.11.2+dfsg-6build5)

Parallel Visualization Application

parsinsert (1.04-15ubuntu1)

Parsimonious Insertion of unclassified sequences into phylogenetic trees

parsinsert-testdata (1.04-15ubuntu1)

Test data for parsinsert

parsnp (2.0.3+dfsg-1ubuntu1 [amd64, arm64, ppc64el, riscv64], 2.0.3+dfsg-1 [armhf])

rapid core genome multi-alignment

patman (1.2.2+dfsg-8)

rapid alignment of short sequences to large databases

pbbamtools (2.4.0+dfsg-1build2)

processing Pacific Biosciences binary alignment/map files

pbdagcon (0.3+git20180411.c14c422+dfsg-8build3)

sequence consensus using directed acyclic graphs

pbhoney (15.8.24+dfsg-7)

genomic structural variation discovery

pbjelly (15.8.24+dfsg-7)

genome assembly upgrading tool

pbsim (1.0.3+git20180330.e014b1d+dfsg-3)

simulator for PacBio sequencing reads

pdb-tools (2.5.1-1)

tools for manipulating and editing PDB files

pdb2pqr (3.6.1+dfsg-1)

Preparation of protein structures for electrostatics calculations

perlprimer (1.2.4-2)

Graphical design of primers for PCR

perlprimer-doc (1.2.4-2)

Tutorial to perlprimer

perm (0.4.0-8)

efficient mapping of short reads with periodic spaced seeds

persalys (15.0+ds-3build5)

GUI for uncertainty treatment and variabilities management

pftools (3.2.12-1)

build and search protein and DNA generalized profiles

phast (1.6+dfsg-4)

phylogenetic analysis with space/time models

phipack (0.0.20160614-5)

PHI test and other tests of recombination

phybin (0.3-6)

binning/clustering newick trees by topology

phylip (1:3.697+dfsg-4build1)

package of programs for inferring phylogenies

phylip-doc (1:3.697+dfsg-4build1)

package of programs for inferring phylogenies (documentation)

phylonium (1.7-3)

Fast and Accurate Estimation of Evolutionary Distances

phyml (3:3.3.20220408-3build2)

Phylogenetic estimation using Maximum Likelihood

physamp (1.1.0-4build2)

sample sequence alignment corresponding to phylogeny

phyutility (2.7.3+dfsg-4)

simple analyses or modifications on both phylogenetic trees and data matrices

phyx (1.3.1+ds-2build1)

UNIX-style phylogenetic analyses on trees and sequences

picard-tools (3.1.1+dfsg-1)

Command line tools to manipulate SAM and BAM files

picopore (1.2.0-3)

lossless compression of Nanopore files

picosat (965-2)

SAT solver with proof and core support

piler (0~20140707-4)

genomic repeat analysis

pilercr (1.06+dfsg-5)

software for finding CRISPR repeats

pilon (1.24-3)

automated genome assembly improvement and variant detection tool

pinfish (0.1.0+ds-4)

Collection of tools to annotate genomes using long read transcriptomics data

pinfish-examples (0.1.0+ds-4)

Examples and test data for pinfish

pique (1.0-7)

software pipeline for performing genome wide association studies

pirs (2.0.2+dfsg-12)

Profile based Illumina pair-end Reads Simulator

pirs-examples (2.0.2+dfsg-12)

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

pirs-profiles (2.0.2+dfsg-12)

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

pizzly (0.37.3+ds-9)

Identifies gene fusions in RNA sequencing data

pkg-r-autopkgtest (20231212ubuntu1)

Script for the automatic testing of R packages

pktools (2.6.7.6+ds-6build1)

GDAL add-on tools to perform useful raster processing

placnet (1.04-1)

Plasmid Constellation Network project

planetary-system-stacker (0.8.32~git20221019.66d7558-2)

create a sharp image of a planetary system object (moon, sun, planets)

planets (0.1.13-22build1)

Gravitation simulation of planetary bodies

plasmidid (1.6.5+dfsg-2)

mapping-based, assembly-assisted plasmid identification tool

plasmidseeker (1.3+dfsg-3)

identification of known plasmids from whole-genome sequencing reads

plast (2.3.2+dfsg-10)

Parallel Local Sequence Alignment Search Tool

plast-example (2.3.2+dfsg-10)

Parallel Local Sequence Alignment Search Tool (example data)

plastimatch (1.9.4+dfsg.1-2build4)

medical image reconstruction and registration

plink (1.07+dfsg-4)

whole-genome association analysis toolset

plink1.9 (1.90~b7.2-231211-1)

whole-genome association analysis toolset

plink2 (2.00~a5.8-231123+dfsg-1)

whole-genome association analysis toolset

pluto-jpl-eph (0.0~git20180228-1.1build1)

command line handling of JPL ephemeres data

pluto-lunar (0.0~git20180825.e34c1d1-1build1)

routines for predictions of positions in solar system

pnetcdf-bin (1.12.3-2build2)

Programs for reading and writing parallel NetCDF files

poa (2.0+20060928-9)

Partial Order Alignment for multiple sequence alignment

populations (1.2.33+svn0120106+dfsg-6ubuntu3)

population genetic software

porechop (0.2.4+dfsg-4)

adapter trimmer for Oxford Nanopore reads

poretools (0.6.0+dfsg-6)

toolkit for nanopore nucleotide sequencing data

poretools-data (0.6.0+dfsg-6)

toolkit for nanopore nucleotide sequencing data -- sample datasets

praat (6.4.06+dfsg-1build2)

program for speech analysis and synthesis

prank (0.0.170427+dfsg-3)

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

predictnls (1.0.20-8)

prediction and analysis of protein nuclear localization signals

prime-phylo (1.0.11-10ubuntu1)

bayesian estimation of gene trees taking the species tree into account

primer3 (2.6.1-4)

tool to design flanking oligo nucleotides for DNA amplification

primer3-examples (2.6.1-4)

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

prinseq-lite (0.20.4-6)

PReprocessing and INformation of SEQuence data (lite version)

prinseq-lite-examples (0.20.4-6)

PReprocessing and INformation of SEQuence data (example data)

proalign (0.603-5)

Probabilistic multiple alignment program

probabel (0.5.0+dfsg-6)

Toolset for Genome-Wide Association Analysis

probabel-examples (0.5.0+dfsg-6)

Example files for ProbABEL

probalign (1.4-10)

multiple sequence alignment using partition function posterior probabilities

probcons (1.12-14)

PROBabilistic CONSistency-based multiple sequence alignment

probcons-extra (1.12-14)

Extra programs from the probcons package

proda (1.0-14)

multiple alignment of protein sequences

prodigal (1:2.6.3-6)

Microbial (bacterial and archaeal) gene finding program

profbval (1.0.22-8)

predictor of flexible/rigid protein residues from sequence

profisis (1.0.11-7)

prediction of protein-protein interaction sites from sequence

profnet-bval (1.0.22-8)

neural network architecture for profbval

profnet-chop (1.0.22-8)

neural network architecture for profchop

profnet-con (1.0.22-8)

neural network architecture for profcon

profnet-isis (1.0.22-8)

neural network architecture for profisis

profnet-md (1.0.22-8)

neural network architecture for metadisorder

profnet-norsnet (1.0.22-8)

neural network architecture for norsnet

profnet-prof (1.0.22-8)

neural network architecture for profacc

profnet-snapfun (1.0.22-8)

neural network architecture for snapfun

profphd-net (1.0.22-8)

neural network architecture for profphd

profphd-utils (1.0.10-7)

profphd helper utilities convert_seq and filter_hssp

proftmb (1.1.12-11)

per-residue prediction of bacterial transmembrane beta barrels

progressivemauve (1.2.0+4713+dfsg-5build3)

multiple genome alignment algorithms

proj-bin (9.4.0-1build2)

Cartographic projection library (tools)

prokka (1.14.6+dfsg-6)

rapid annotation of prokaryotic genomes

promod3 (3.4.0+ds-1)

protein homology modelling engine

promod3-data (3.4.0+ds-1)

protein homology modelling engine - data files

proteinortho (6.3.1+dfsg-1)

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

prottest (3.4.2+dfsg-8)

selection of best-fit models of protein evolution

provean (1.1.5+ds-2)

Protein Variation Effect Analyzer

pscan-chip (1.1-3build1)

ChIP-based identifcation of TF binding sites

pscan-chip-data (1.1-3build1)

auxiliary data for PScan-ChIP

pscan-tfbs (1.2.2-4build1)

search for transcription factor binding sites

psfex (3.24.2-1)

Point Spread Function model extractor

psi3 (3.4.0-6ubuntu1)

Quantum Chemical Program Suite

psi4 (1:1.3.2+dfsg-5build3)

Quantum Chemical Program Suite

psi4-data (1:1.3.2+dfsg-5build3)

Quantum Chemical Program Suite (data files)

psortb (3.0.6+dfsg-3build4)

bacterial localization prediction tool

psychopy (2023.2.4+dfsg-3)

environment for creating psychology stimuli in Python

psychtoolbox-3-common (3.0.19.5.dfsg1-1build3)

toolbox for vision research -- arch/interpreter independent part

psychtoolbox-3-lib (3.0.19.5.dfsg1-1build3)

toolbox for vision research -- arch-specific parts

pullseq (1.0.2-5)

Extract sequence from a fasta or fastq

pycoqc (2.5.2+dfsg-3)

computes metrics and generates Interactive QC plots

pyensembl (2.3.9-2)

installs data from the Ensembl genome database

pyfai (2024.02-1build2)

Fast Azimuthal Integration scripts

pyfastx (2.0.2-2)

fast random access to sequences from FASTA/Q file - command

pyfr (1.5.0-3)

flux reconstruction in Python

pymca (5.9.2+dfsg-2build1)

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

pymca-data (5.9.2+dfsg-2build1)

Architecture independent data files for PyMca

pymoctool (0.5.0-5)

Python Multi-Order Coverage maps tool for Virtual Observatory

pymol (2.5.0+dfsg-1build6)

Molecular Graphics System

pymol-data (2.5.0+dfsg-1build6)

data files for PyMOL

pyomop (4.2.0-1)

OHSDI OMOP Common Data Model tools

python-drizzle-testdata (1.15.0-1build1)

Dithered image combination for Python (Test data)

python-escript-doc (5.6-6build3)

Documentation for Escript/Finley

python-pairix-examples (0.3.7-7build1)

1D/2D indexing and querying with a pair of genomic coordinates (examples)

python3-airr (1.5.0-1)

Data Representation Standard library for antibody and TCR sequences

python3-alignlib (0.1.1+dfsg-2build5)

edit and Hamming distances for biological sequences

python3-amp (0.6.1-1build9)

Atomistic Machine-learning Package (python 3)

python3-bioframe (0.4.1-1)

library to enable flexible, scalable operations on genomic interval dataframes

python3-bornagain (21.1+ds3-4)

Simulate and fit X-ray and neutron GISAS -- Python3

python3-cif2cell (2.1.0+dfsg-1)

prepare CIF files for electronic structure calculations

python3-cykhash (2.0.0-3build1)

cython wrapper for khash-sets/maps, efficient implementation of isin and unique

python3-datalad-next (1.2.0-1)

DataLad extension for new features and improved user experience

python3-dcmstack (0.9-1ubuntu1)

DICOM to NIfTI conversion - python3 package

python3-dials (3.17.0+dfsg3-3build3)

Diffraction Integration for Advanced Light Sources - Python3

python3-emperor (1.0.3+ds-9)

visualizing high-throughput microbial community data

python3-escript (5.6-6build3)

Escript/Finley finite elements Python3 system (with OpenMP)

python3-escript-mpi (5.6-6build3)

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

python3-gfapy (1.2.3+dfsg-2)

flexible and extensible software library for handling sequence graphs

python3-gffutils (0.13-1)

Work with GFF and GTF files in a flexible database framework

python3-gtfparse (1.3.0+ds-1)

parser for gene transfer format (aka GFF2)

python3-harmonypy (0.0.9-2)

is a data integration algorithm

python3-jupyter-sphinx (0.3.2-2)

Jupyter Sphinx Extension - Python3

python3-louvain (0.0+20181013git3fc1f575-2)

community graph analysis implementing Louvain method

python3-mmtf (1.1.3-1)

binary encoding of biological structures (Python 3)

python3-mpiplus (0.0.2+ds-1)

Python GPU framework for alchemical free energy calculations (Python 3)

python3-navarp (1.6.0-2)

Navigation tool for ARPES data (Python 3)

python3-noise (1.2.3-4build4)

Perlin noise for image generation

python3-onnx (1.14.1-2.1build2)

Open Neural Network Exchange (ONNX) (Python)

python3-parmed (4.2.2+dfsg-3build1)

parameter and topology file editor and molecular mechanical simulator

python3-pdbtools (2.5.1-1)

tools for manipulating and editing PDB files (Python 3 package)

python3-peptidebuilder (1.1.0-3)

generate atomic oligopeptide 3D structure from sequence

python3-prodigy (2.1.5-1)

Protein Binding Affinity Prediction (Python 3)

python3-prody (2.4.1+dfsg-2)

Python package for protein dynamics analysis

python3-prody-tests (2.4.1+dfsg-2)

Python package for protein dynamics analysis - test data

python3-py2bit (0.3.1-2build1)

access to 2bit files

python3-pyaml-env (1.2.1-1)

Python3 YAML configuration with environment variables parsing

python3-pybel (0.14.10-1)

Biological Expression Language

python3-pybigwig (0.3.22+dfsg-1build3)

Python 3 module for quick access to bigBed and bigWig files

python3-pyimagetool (1.0-2)

Image Tool for multidimensional analysis (Python 3)

python3-pymbar (3.1.0-4)

Python implementation of the multistate Bennett acceptance ratio (MBAR)

python3-pynlpl (1.2.9-1)

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

python3-pyxrd (0.8.4-3)

modeling of X-ray diffraction (XRD) patterns of disordered lamellar structures

python3-qiskit-terra (0.12.0-4build3)

Quantum Information Science Kit (Qiskit) for Python 3

python3-tinyalign (0.2.2-1build2)

numerical representation of differences between strings

python3-weblogo (3.7.12-5)

sequence logo generator

python3-xeus-python-shell (0.15.10+~0.6.1-2build2)

Native jupyter kernel for python (python library)

python3-xraydb (4.5.3-2)

X-ray Reference Data (Python 3)

python3-xrt (1.6.0+ds1-1)

XRay Tracer and wave propagation (Python 3)

pyzo (4.12.3-1)

interactive editor for scientific Python

q2templates (2024.2.0+ds-1)

Design template package for QIIME 2 Plugins

qcat (1.1.0-6)

demultiplexing Oxford Nanopore reads from FASTQ files

qcat-examples (1.1.0-6)

demultiplexing Oxford Nanopore reads from FASTQ files (examples)

qcumber (2.3.0-2)

quality control of genomic sequences

qemu-web-desktop (24.01.19+ds1-3)

Remote desktop service with virtual machines in a browser.

qfits-tools (6.2.0-9ubuntu1)

FITS manipulation tools

qfitsview (4.1+dfsg-2build3)

FITS file viewer based on DPUSER

qgis (3.34.4+dfsg-4build2)

Geographic Information System (GIS)

qgis-api-doc (3.34.4+dfsg-4build2)

QGIS API documentation

qgis-common (3.34.4+dfsg-4build2)

QGIS - architecture-independent data

qgis-plugin-grass (3.34.4+dfsg-4build2)

GRASS plugin for QGIS

qgis-plugin-grass-common (3.34.4+dfsg-4build2)

GRASS plugin for QGIS - architecture-independent data

qgis-provider-grass (3.34.4+dfsg-4build2)

GRASS provider for QGIS

qgis-providers (3.34.4+dfsg-4build2)

collection of data providers to QGIS

qgis-providers-common (3.34.4+dfsg-4build2)

collection of data providers to QGIS - architecture-independent files

qgis-server (3.34.4+dfsg-4build2)

QGIS server providing various OGC services

qgis-server-bin (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (executables)

qgis-server-common (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (data)

qgis-server-dummy (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (dummy)

qgis-server-landingpage (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (landing page)

qgis-server-wcs (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (WCS)

qgis-server-wfs (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (WFS)

qgis-server-wfs3 (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (WFS 3)

qgis-server-wms (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (WMS)

qgis-server-wmts (3.34.4+dfsg-4build2)

QGIS server providing various OGC services (WMTS)

qgis3-survex-import (1.3-1)

QGIS3 plugin to read survex 3d files, for cave surveying

qmapshack (1.17.1-1build2)

GPS mapping (GeoTiff and vector) and GPSr management

qmc (0.94-4.1)

Quine McClusky Simplification Tool

qrisk2 (0.1.20150729-5)

cardiovascular disease risk calculator

qthid-fcd-controller (4.1-6build2)

Funcube Dongle controller

qtltools (1.3.1+dfsg-4build3)

Tool set for molecular QTL discovery and analysis

qttinysa (0.10.1-1)

QT Gui for a tiny SA Spectrum Analyser

quantum-espresso (6.7-2build4)

Electronic-Structure and Ab-Initio Molecular Dynamics Suite

quantum-espresso-data (6.7-2build4)

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

quantum-espresso-data-sssp (1.3.0-2)

Standard solid-state pseudopotentials (SSSP) library

quicktree (2.5-6)

Neighbor-Joining algorithm for phylogenies

quorum (1.1.2-2)

QUality Optimized Reads of genomic sequences

qutemol (0.4.1~cvs20081111-15build2)

interactive visualization of macromolecules

r-cran-colorspace (2.1-0+dfsg-1)

GNU R Color Space Manipulation

r-cran-epibasix (1.5-2build1)

GNU R Elementary Epidemiological Functions

r-cran-genetics (1.3.8.1.3-1)

GNU R package for population genetics

r-cran-haplo.stats (1.9.5.1-1)

GNU R package for haplotype analysis

r-cran-maptools (1:1.1-8+dfsg-1)

GNU R Tools for reading and handling spatial objects

r-cran-msm (1.7.1-1)

GNU R Multi-state Markov and hidden Markov models in continuous time

r-cran-randomforest (4.7-1.1-1)

GNU R package implementing the random forest classificator

r-cran-sdmtools (1.1-221.2-1build1)

Species Distribution Modelling Tools

r-cran-sp (1:2.1-2+dfsg-1)

GNU R classes and methods for spatial data

r-cran-spc (1:0.6.7-1)

GNU R Statistical Process Control

r-cran-vcd (1:1.4-12-1)

GNU R Visualizing Categorical Data

r-cran-xtable (1:1.8-4-2)

GNU R coerce data to LaTeX and HTML tables

racon (1.5.0-3)

consensus module for raw de novo DNA assembly of long uncorrected reads

radiant (2.8.1+dfsg-2)

explore hierarchical metagenomic data with zoomable pie charts

ragout (2.3-5)

Reference-Assisted Genome Ordering UTility

ragout-examples (2.3-5)

Reference-Assisted Genome Ordering UTility (example data)

rambo-k (1.21+dfsg-4)

Read Assignment Method Based On K-mers

rampler (2.1.1-1)

module for sampling genomic sequences

rapmap (0.15.0+dfsg-3)

rapid sensitive and accurate DNA read mapping via quasi-mapping

rapmap-dev (0.15.0+dfsg-3)

rapmap - rapid sensitive and accurate DNA read mapping (some headers)

rapmap-example-data (0.15.0+dfsg-3)

example data for rapmap - rapid sensitive and accurate DNA read mapping

rasmol (2.7.6.0-3build3)

visualization of biological macromolecules

rasmol-doc (2.7.6.0-3build3)

documentation for rasmol

rate4site (3.0.0-8)

detector of conserved amino-acid sites

rawtran (1.1-1build5)

RAW photo to FITS converter

raxml (8.2.13+dfsg-1)

Randomized Axelerated Maximum Likelihood of phylogenetic trees

ray (2.3.1-8build2)

de novo genome assemblies of next-gen sequencing data

ray-extra (2.3.1-8build2)

Scripts and XSL sheets for post-processing for ray

rdkit-data (202309.3-3build2)

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

rdp-classifier (2.10.2-7)

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

readseq (1-15)

Conversion between sequence formats

readucks (0.0.3-5)

Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)

reapr (1.0.18+dfsg-5ubuntu2)

universal tool for genome assembly evaluation

recan (0.5+dfsg-1)

genetic distance plotting for recombination events analysis

refmac-dictionary (5.41-2)

dictionary for macromolecular refinement and model building

relion (3.1.3-3build3)

toolkit for 3D reconstructions in cryo-electron microscopy

relion-gui (3.1.3-3build3)

toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)

repeatmasker-recon (1.08-8)

finds repeat families from biological sequences

reprof (1.0.1-8)

protein secondary structure and accessibility predictor

resfinder (4.4.2-1)

identify acquired antimicrobial resistance genes

resfinder-db (0.0+git20220524.fa32d9a-1)

ResFinder database is a curated database of acquired resistance genes

resfinder-example (4.4.2-1)

identify acquired antimicrobial resistance genes (example data)

rna-star (2.7.11b+dfsg-1build1)

ultrafast universal RNA-seq aligner

rnahybrid (2.1.2-8)

Fast and effective prediction of microRNA/target duplexes

roary (3.13.0+dfsg-1)

high speed stand alone pan genome pipeline

rocketcea (1.1.34+dfsg-2)

NASA Chemical Equilibrium, wrapped in Python

rockhopper (2.0.3+dfsg2-4)

system for analyzing bacterial RNA-seq data

rocs (4:23.08.5-0ubuntu4)

graph theory IDE

roguenarok (1.0.1-3)

versatile and scalable algorithm for rogue taxon identification

routine-update (0.2)

routine updater for a Debian source package

rsem (1.3.3+dfsg-3build1)

RNA-Seq by Expectation-Maximization

rtax (0.984-8)

Classification of sequence reads of 16S ribosomal RNA gene

ruby-getspg (2.3.1-1ubuntu2)

C library for crystal symmetry determination - Ruby bindings

runcircos-gui (0.0+git20200528.82dda8c-1build2)

GUI tool to run circos

sac2mseed (1.13+ds1-1build1)

Convert SAC waveform data to MiniSEED

saga (9.3.1+dfsg-3build3)

System for Automated Geoscientific Analyses

saga-common (9.3.1+dfsg-3build3)

SAGA GIS architecture independent files

saint (2.5.0+dfsg-4build1)

Significance Analysis of INTeractome

salmid (0.1.23-5)

rapid Kmer based Salmonella identifier from sequence data

salmon (1.10.2+ds1-1build2)

wicked-fast transcript quantification from RNA-seq data

sambamba (1.0.1+dfsg-1build3)

tools for working with SAM/BAM data

samblaster (0.1.26-4)

marks duplicates, extracts discordant/split reads

samclip (0.4.0-4)

filter SAM file for soft and hard clipped alignments

samtools (1.19.2-1build2)

processing sequence alignments in SAM, BAM and CRAM formats

samtools-test (1.19.2-1build2)

test files for the samtools package

saods9 (8.5+repack-1build2)

Image display tool for astronomy

sasview (5.0.6-2)

Small Angle Scattering Analysis suite

sat4j (2.3.5-0.3)

Efficient library of SAT solvers in Java

savi (1.6.0-1)

satellite constellation visualisation

savvy-util (2.1.0-2)

conversion tool for SAV file format

sbmltoolbox (4.1.0-5ubuntu1)

libsbml toolbox for octave and matlab

scamp (2.10.0-2build2)

Compute astrometric and photometric solutions

science-distributedcomputing (1.14.5ubuntu1)

Debian Science Distributed Computing packages

science-electrophysiology (1.14.5ubuntu1)

Debian Science packages for Electrophysiology

science-highenergy-physics (1.14.5ubuntu1)

Debian Science High Energy Physics packages

science-highenergy-physics-dev (1.14.5ubuntu1)

Debian Science High Energy Physics development packages

science-machine-learning (1.14.5ubuntu1)

Debian Science Machine Learning packages

science-nanoscale-physics (1.14.5ubuntu1)

Debian Science Nanoscale Physics packages

science-nanoscale-physics-dev (1.14.5ubuntu1)

Debian Science Nanoscale Physics development packages

science-neuroscience-modeling (1.14.5ubuntu1)

Debian Science packages for modeling of neural systems

science-physics-dev (1.14.5ubuntu1)

Debian Science Physics-dev packages

science-psychophysics (1.14.5ubuntu1)

Debian Science packages for Psychophysics

science-simulations (1.14.5ubuntu1)

Debian Science Simulation packages

scoary (1.6.16-6)

pangenome-wide association studies

scram (0.16.2-3build4)

Probabilistic Risk Analysis Tool

scram-gui (0.16.2-3build4)

SCRAM GUI front-end

scrappie (1.4.2-8build2)

basecaller for Nanopore sequencer

scrm (1.7.4-1)

simulator of evolution of genetic sequences

sctk (2.4.10-20151007-1312Z+dfsg2-3.1)

speech recognition scoring toolkit

scythe (0.994+git20141017.20d3cff-3)

Bayesian adaptor trimmer for sequencing reads

secrecy (0.0.5+ds-3build2)

tool to handle libsecrecy keys and encrypted files

seer (1.1.4-7build4)

genomic sequence element (kmer) enrichment analysis

segemehl (0.3.4-5build2)

short read mapping with gaps

sentencepiece (0.2.0-1build1)

Unsupervised text tokenizer and detokenizer

seq-gen (1.3.4-2)

simulate the evolution of nucleotide or amino acid sequences

seqan-needle (1.0.2+ds-2)

pre-filter for the counting of very large collections of nucleotide sequences

seqan-raptor (3.0.1+ds-5)

pre-filter for querying very large collections of nucleotide sequences

seqkit (2.3.1+ds-2)

cross-platform and ultrafast toolkit for FASTA/Q file manipulation

seqkit-examples (2.3.1+ds-2)

examples for seqkit: toolkit for FASTA/Q file manipulation

seqmagick (0.8.6-1)

imagemagick-like frontend to Biopython SeqIO

seqprep (1.3.2-9)

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

seqprep-data (1.3.2-9)

example data set for seqprep - only used for testing

seqsero (1.0.1+dfsg-6)

Salmonella serotyping from genome sequencing data

seqtk (1.4-2)

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

seriation (0.1+git20210125.fc7b8cb-1)

finds a suitable linear order for a set of objects

seriation-data (0.1+git20210125.fc7b8cb-1)

test data for seriation

sga (0.10.15-7build1)

de novo genome assembler that uses string graphs

shapeit4 (4.2.2+dfsg-1build3)

fast and accurate method for estimation of haplotypes (phasing)

shasta (0.11.1-4build4)

nanopore whole genome assembly (binaries and scripts)

shelxle (1.0.1552-1build2)

graphical user interface for SHELXL

shiny-server (1.5.20.1002-2build1)

put Shiny web apps online

shovill (1.1.0-9)

Assemble bacterial isolate genomes from Illumina paired-end reads

shovill-examples (1.1.0-9)

Test Data for shovill

sibelia (3.0.7+dfsg-3)

comparative genomics tool

sibelia-examples (3.0.7+dfsg-3)

comparative genomics tool (example data)

sibsim4 (0.20-5)

align expressed RNA sequences on a DNA template

sickle (1.33+git20150314.f3d6ae3-2)

windowed adaptive trimming tool for FASTQ files using quality

siconos (4.4.0+dfsg-4)

modeling and simulation of nonsmooth dynamical systems (simulation runner tool)

siconos-mechanics-tools (4.4.0+dfsg-4)

modeling and simulation of nonsmooth dynamical systems (mechanics tools)

sightcalibrator (23.1.0-2build5)

Camera calibration software

sightviewer (23.1.0-2build5)

DICOM viewer

sigma-align (1.1.3-9build1)

Simple greedy multiple alignment of non-coding DNA sequences

sigviewer (0.6.4-3build2)

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

silx (2.0.1+dfsg-3)

Toolbox for X-Ray data analysis - Executables

sim4 (0.0.20121010-8)

tool for aligning cDNA and genomic DNA

sim4db (0~20150903+r2013-8build4)

batch spliced alignment of cDNA sequences to a target genome

simka (1.5.3-8build2)

comparative metagenomics method dedicated to NGS datasets

simkamin (1.5.3-8build2)

approximate comparative metagenomics method dedicated to NGS datasets

simrisc (15.05.00-1build1)

simulation model for breast/lung cancer risk

siril (1.2.1-1build3)

astronomical image processing tool

siril-common (1.2.1-1build3)

architecture-independent files for siril

ska (1.0+dfsg-4)

Split Kmer Analysis

skesa (2.4.0-6build2)

strategic Kmer extension for scrupulous assemblies

skewer (0.2.2-6)

post-processing of high-throughput DNA sequence reads

skycat (3.1.2+starlink1~b+dfsg-7build3)

Image visualization and access to catalogs and data for astronomy

slang-xfig (0.2.0~.138-1)

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

smalt (0.7.6-13)

Sequence Mapping and Alignment Tool

smalt-examples (0.7.6-13)

Sequence Mapping and Alignment Tool (examples)

smiles-scripts (0.2.0+dfsg1-5)

command line tools to handle SMILES descriptors

smithwaterman (0.0+git20160702.2610e25-12)

determine similar regions between two strings or genomic sequences

smrtanalysis (0~20210112)

software suite for single molecule, real-time sequencing

snakemake (7.32.4-2)

pythonic workflow management system

snap (2013-11-29-11)

location of genes from DNA sequence with hidden markov model

snap-aligner (2.0.3+dfsg-2)

Scalable Nucleotide Alignment Program

sniffles (2.2-1)

structural variation caller using third-generation sequencing

snippy (4.6.0+dfsg-4)

rapid haploid variant calling and core genome alignment

snippy-examples (4.6.0+dfsg-4)

rapid haploid variant calling and core genome alignment (examples)

snp-sites (2.5.1-2)

Binary code for the package snp-sites

snpomatic (1.0-7)

fast, stringent short-read mapping software

soapaligner (2.20-5)

aligner of short reads of next generation sequencers

soapdenovo (1.05-6)

short-read assembly method to build de novo draft assembly

soapdenovo2 (242+dfsg-3)

short-read assembly method to build de novo draft assembly

soapsnp (1.03-5)

resequencing utility that can assemble consensus sequence of genomes

sortmerna (4.3.6-3build2)

tool for filtering, mapping and OTU-picking NGS reads

source-extractor (2.28.0+ds-1build2)

Source extractor for astronomical images

sp800-90b-entropy-assessment (1.1.5-4build2)

Estimating the quality of a source of entropy

spaced (1.2.0-201605+dfsg-4)

alignment-free sequence comparison using spaced words

spades (3.15.5+dfsg-7)

genome assembler for single-cell and isolates data sets

spaln (2.4.13f+dfsg-1)

splicing-aware transcript-alignment to genomic DNA

spaln-data (2.4.13f+dfsg-1)

splicing-aware transcript-alignment to genomic DNA (data)

spass (3.9-1.1)

automated theorem prover for first-order logic with equality

spatialite-bin (5.1.0a-1build2)

Geospatial extension for SQLite - tools

spd (1.3.0-1.1)

Synchrotron image corrections and azimuthal integration

splash (3.10.1-2)

Visualisation tool for Smoothed Particle Hydrodynamics simulation

spoa (4.0.8-1)

SIMD partial order alignment tool

sprai (0.9.9.23+dfsg1-2)

single-pass sequencing read accuracy improver

spview (2.0.2-1)

Spectrum Viewer

squizz (0.99d+dfsg-3)

Converter for genetic sequences and alignments

sra-toolkit (3.0.3+dfsg-6ubuntu5)

utilities for the NCBI Sequence Read Archive

srst2 (0.2.0-11)

Short Read Sequence Typing for Bacterial Pathogens

ssake (4.0.1-1)

genomics application for assembling millions of very short DNA sequences

ssake-examples (4.0.1-1)

example data for SSAKE, a genomic assembler of short reads

sspace (2.1.1+dfsg-7)

scaffolding pre-assembled contigs after extension

ssshtest (0.0+git20220105.0d6df3d-1)

stupid simple (ba)sh testing

ssw-align (1.1-14build1)

Smith-Waterman aligner based on libssw

stacks (2.66+dfsg-1build2)

pipeline for building loci from short-read DNA sequences

staden (2.0.0+b11-5)

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

staden-common (2.0.0+b11-5)

Architecture independent files for Staden

staden-io-lib-examples (1.15.0-1.1build2)

programs for manipulating DNA sequencing files (usage examples)

staden-io-lib-utils (1.15.0-1.1build2)

programs for manipulating DNA sequencing files

stardata-common (0.8+nmu1)

Common framework to manage astronomy packages

starpu-examples (1.4.3+dfsg-5build1)

Task scheduler for heterogeneous multicore machines - exs

stellarium (23.4-2build3)

real-time photo-realistic sky generator

stellarium-data (23.4-2build3)

Stellarium data files

stiff (2.4.0-7build1)

convert scientific FITS images to the TIFF format

stilts (3.4.9-5)

Starlink Tables Infrastructure Library Tool Set

stimfit (0.16.0-1.2build4)

Program for viewing and analyzing electrophysiological data

stringtie (2.2.1+ds-3build2)

assemble short RNAseq reads to transcripts

subarch-select (0.2-1)

Select among binaries based upon x86 microarchitecture support

subread (2.0.6+dfsg-2)

toolkit for processing next-gen sequencing data

subread-data (2.0.6+dfsg-2)

data files for subread package

suitename (0.4.130509+git20210223.ebb1325-1)

categorize each suite in an RNA backbone

sumaclust (1.0.36+ds-2)

fast and exact clustering of genomic sequences

sumatra (1.0.36+ds-2)

fast and exact comparison and clustering of sequences

sumo (1.18.0+dfsg-3build5)

Simulation of Urban MObility (SUMO)

surankco (0.0.r5+dfsg-4)

Supervised Ranking of Contigs in de novo Assemblies

surpyvor (0.5-2)

modification of VCF files with SURVIVOR

survex (1.4.4-1build3)

cave surveying and mapping software

survex-aven (1.4.4-1build3)

sophisticated cave survey viewer for Survex

survivor (1.0.7-4)

tool set for simulating/evaluating SVs

svim (2.0.0-3)

Structural variant caller for long sequencing reads

swarm (3.1.4+dfsg-1)

robust and fast clustering method for amplicon-based studies

swarp (2.41.5-1build3)

Resample and co-add together FITS images

swe-basic-data (4.0-20221111-2)

Swiss Ephemeris library (basic set of ephemeris files).

swe-standard-data (4.0-20221111-2)

Swiss Ephemeris library (standard set of ephemeris files).

sweed (3.2.1+dfsg-5)

assessment of SNPs for their evolutionary advantage

syrthes (4.3.5+20200129-dfsg1-1build2)

Transient thermal simulations in complex solid geometries

syrthes-gui (4.3.5+20200129-dfsg1-1build2)

Transient thermal simulations in complex solid geometries - GUI

syrthes-tests (4.3.5+20200129-dfsg1-1build2)

Test cases for SYRTHES

syrthes-tools (4.3.5+20200129-dfsg1-1build2)

Transient thermal simulations in complex solid geometries - tools

t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1)

Multiple Sequence Alignment

t-coffee-examples (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1)

annotated examples for the use of T-Coffee

tabix (1.19+ds-1.1build3)

generic indexer for TAB-delimited genome position files

tandem-mass (1:201702011-1build1)

mass spectrometry software for protein identification

tantan (49-1)

low complexity and tandem repeat masker for biosequences

tcd-utils (20061127-2.1)

convert Tide Constituent Database (TCD) files

tcl-fitstcl (2.5-2build2)

Tcl interface to FITS files

tclfitsy (8.5+repack-1build2)

Tcl FITS Extension

terraintool (1.16-3)

Generates survex/therion terrain models from SRTM/NASADEM data.

theli (3.1.4-1ubuntu2)

Astronomical image data reduction pipeline

therion (6.2.0-1build3)

Cave surveying - 2D and 3D drawing software

therion-doc (6.2.0-1build3)

Documentation for Therion Cave surveying software

therion-viewer (6.2.0-1build3)

Cave surveying - 3D viewer for therion models

theseus (3.3.0-14)

superimpose macromolecules using maximum likelihood

theseus-examples (3.3.0-14)

superimpose macromolecules using maximum likelihood (examples)

thesias (3.1.1-1)

Testing Haplotype Effects In Association Studies

threeb (0.0~git20220106110332.a3144e0-6build1)

3B Microscopy Analysis Software - command-line tool

threeb-imagej (0.0~git20220106110332.a3144e0-6build1)

3B Microscopy Analysis Software - ImageJ plugin

tiddit (3.6.1+dfsg-1build1)

structural variant calling

tigr-glimmer (3.02b-6)

Gene detection in archea and bacteria

timbl (6.5-3.1build2)

Tilburg Memory Based Learner

timblserver (1.14-3.1build2)

Server extensions for Timbl

tiny-dnn (1.0.0a3+ds-4)

header only deep learning framework in C++

tippecanoe (2.49.0-1build1)

build vector tilesets from large collections of GeoJSON features

tksao (8.5+repack-1build2)

Tk widgets for astronomical imaging and data visualization

tm-align (20190822+dfsg-2build1)

structural alignment of proteins

tnseq-transit (3.3.4-1)

statistical calculations of essentiality of genes or genomic regions

tombo (1.5.1-6build1)

identification of modified nucleotides from raw nanopore sequencing data

topcat (4.9-1)

Tool for OPerations on Catalogues And Tables

tophat-recondition (1.4-3)

post-processor for TopHat unmapped reads

topp (2.6.0+cleaned1-4build4)

set of programs implementing The OpenMS Proteomic Pipeline

topparser (1.3-3)

Conversion utility from pockettopo to therion, for cave surveying

toppic (1.5.3+dfsg1-1build3)

Top-down proteoform identification and characterization (programs)

toppic-common (1.5.3+dfsg1-1build3)

Top-down proteoform identification and characterization (common data)

toppred (1.10-10)

transmembrane topology prediction

tortoize (2.0.11-1)

Application to calculate ramachandran z-scores

toulbar2 (1.2.1+dfsg-0.1)

Exact combinatorial optimization for Graphical Models

toulbar2-doc (1.2.1+dfsg-0.1)

Exact combinatorial optimization for Graphical Models - documentation

trace2dbest (3.0.1-2)

bulk submission of chromatogram data to dbEST

trace2dbest-doc (3.0.1-2)

Documentation and sample files for trace2dbest

tracetuner (3.0.6~beta+dfsg-3)

interpretation of DNA Sanger sequencing data

transdecoder (5.7.1-2)

find coding regions within RNA transcript sequences

transfuse (0.5.8-1build4)

Runs formatted documents through transformations/translation

transrate-tools (1.0.0-5)

helper for transrate

transtermhp (2.09-5)

find rho-independent transcription terminators in bacterial genomes

travis (220729-1)

trajectory analyzer and visualizer

tree-ppuzzle (5.3~rc16+dfsg-9build2)

Parallelized reconstruction of phylogenetic trees by maximum likelihood

tree-puzzle (5.3~rc16+dfsg-9build2)

Reconstruction of phylogenetic trees by maximum likelihood

tree-puzzle-doc (5.3~rc16+dfsg-9build2)

Reconstruction of phylogenetic trees by maximum likelihood (doc)

treeviewx (0.5.1+git20100823.7e4d0e9-4build3)

Displays and prints phylogenetic trees

trf (4.09.1-6)

locate and display tandem repeats in DNA sequences

trf-examples (4.09.1-6)

locate and display tandem repeats in DNA sequences (examples)

trim-galore (0.6.10-1)

automate quality and adapter trimming for DNA sequencing

trimmomatic (0.39+dfsg-2)

flexible read trimming tool for Illumina NGS data

trinculo (0.96+dfsg-4)

toolkit to carry out genetic association for multi-category phenotypes

trinityrnaseq (2.15.1+dfsg-5build1)

RNA-Seq De novo Assembly

trinityrnaseq-examples (2.15.1+dfsg-5build1)

RNA-Seq De novo Assembly common example and testing files

tunnelx (20190701-1)

Cave Survey drawing software

tvc (5.0.3+git20151221.80e144e+dfsg-5build2)

genetic variant caller for Ion Torrent sequencing platforms

twms (0.07z+git20201202+bb7c3f8-2)

tiny web map service

twopaco (1.0.0+dfsg-1)

build the compacted de Bruijn graph from many complete genomes

ubertooth (2018.12.R1-5.1)

2.4 GHz wireless development platform for Bluetooth experimentation

ubertooth-firmware (2018.12.R1-5.1)

Firmware for Ubertooth

ubertooth-firmware-source (2018.12.R1-5.1)

Source code for the Ubertooth firmware

uc-echo (1.12-18)

error correction algorithm designed for short-reads from NGS

ucto (0.21.1-2.1build2)

Unicode Tokenizer

uctodata (0.8-2)

Data files for Ucto

ucx-utils (1.16.0+ds-5ubuntu1)

Utilities for the UCX messaging library

uhd-doc (4.6.0.0+ds1-5.1build4)

universal hardware driver for Ettus Research products - doc

uhd-host (4.6.0.0+ds1-5.1build4)

universal hardware driver for Ettus Research products - host apps

umis (1.0.9-1build1)

tools for processing UMI RNA-tag data

umis-examples (1.0.9-1build1)

tools for processing UMI RNA-tag data (examples)

uncalled (2.3+ds-1build3)

Utility for Nanopore Current Alignment to Large Expanses of DNA

unicycler (0.5.0+dfsg-1)

hybrid assembly pipeline for bacterial genomes

unicycler-data (0.5.0+dfsg-1)

hybrid assembly pipeline for bacterial genomes (data package)

unifrac-tools (1.4-3build2)

high-performance phylogenetic diversity calculations (binaries)

unihedron-device-manager (1.0.0.337-1build2)

Unihedron Device manager (UDM)

unikmer (0.19.1-1build1)

Toolkit for nucleic acid k-mer analysis

units-filter (4.2.1-1)

Parser for expressions concerning physical values

units-master (4.2.1-1)

Powerful units converter with a GUI

v-sim (3.7.2-9build3)

Visualize atomic structures

v-sim-common (3.7.2-9build3)

Visualize atomic structures (support files)

v-sim-plugins (3.7.2-9build3)

Plugins for V_Sim (a 3D visualization package)

varna (3-93+ds-5)

Visualization Applet for RNA

vcfanno (0.3.5+ds-2)

annotate a VCF with other VCFs/BEDs/tabixed files

vcfanno-examples (0.3.5+ds-2)

examples for vcfanno: annotate a VCF with other VCFs/BEDs/tabixed files

vcftools (0.1.16-3)

Collection of tools to work with VCF files

velvet (1.2.10+dfsg1-8)

Nucleic acid sequence assembler for very short reads

velvet-example (1.2.10+dfsg1-8)

Example data for the Velvet sequence assembler

velvet-long (1.2.10+dfsg1-8)

Nucleic acid sequence assembler for very short reads, long version

velvet-tests (1.2.10+dfsg1-8)

Test data for the Velvet sequence assembler

velvetoptimiser (2.2.6-5)

automatically optimise Velvet do novo assembly parameters

veryfasttree (4.0.3+dfsg-1)

Speeding up the estimation of phylogenetic trees from sequences

veusz (3.6.2-1.1)

2D and 3D scientific plotting application with graphical interface

virulencefinder (2.0.5-1ubuntu1)

identify virulence genes in total or partial sequenced isolates of bacteria

virulencefinder-examples (2.0.5-1ubuntu1)

example data for virulencefinder

visp-images-data (3.6.0-1)

visual servoing library - dataset reference files

vistrails (3.0~git+9dc22bd.dfsg.1-2)

Science visualisation workflow toolkit

vmatch (2.3.1+dfsg-9)

large scale sequence analysis software

voro++ (0.5+revert-to-0.4.6+dfsg1-1)

library for the computation of the Voronoi diagram

voro++-examples (0.5+revert-to-0.4.6+dfsg1-1)

library for the computation of the Voronoi diagram (examples)

voronota (1.22.3149-2)

Voronoi diagram-based tool to find atom contacts

votca (2023-1build2)

Molecular dynamics analysis - coarse-graining and charge transport

votca-data (2023-1build2)

VOTCA molecular dynamics analysis - basis sets and scripts

votca-tutorials (2023-1build2)

VOTCA molecular dynamics analysis - tutorials

vowpal-wabbit (8.6.1.dfsg1-1build3)

fast and scalable online machine learning algorithm

vsearch (2.27.0-1)

tool for processing metagenomic sequences

vsearch-examples (2.27.0-1)

Test Data for vsearch tool for processing metagenomic sequences

vt (0.57721+ds-3build2)

toolset for short variant discovery in genetic sequence data

vt-examples (0.57721+ds-3build2)

toolset for short variant discovery in genetic sequence data (examples)

wcslib-tools (8.2.2+ds-3build2)

Command line tools utilizing wcslib

wcstools (3.9.7-1.1build1)

Handle the WCS of a FITS image

weightwatcher (1.12+dfsg-3)

Combine maps and polygon data for astronomical image processing

weka (3.6.14-4)

Machine learning algorithms for data mining tasks

wham-align (0.1.5-8)

Wisconsin's High-Throughput Alignment Method

wigeon (20101212+dfsg1-6)

reimplementation of the Pintail 16S DNA anomaly detection utility

wise (2.4.1-24build1)

comparison of biopolymers, like DNA and protein sequences

wsclean (3.4-1build3)

Fast generic widefield interferometric imager

wtdbg2 (2.5-9)

de novo sequence assembler for long noisy reads

wtdbg2-examples (2.5-9)

Examples for wtdbg - de novo sequence assembler

wxastrocapture (1.8.1+git20140821.796e1a1+dfsg-2build3)

Windows linuX Astronomy Capture

xbs (0-11)

3-d models and movies of molecules

xcas (1.9.0.93+dfsg2-2)

Computer Algebra System - console and graphical calculator

xcrysden (1.6.2-4)

Crystalline and Molecular Structure Visualizer

xcrysden-data (1.6.2-4)

Crystalline and Molecular Structure Visualizer (Data Files)

xeus-python-dev (0.15.10+~0.6.1-2build2)

Native jupyter kernel for python (headers)

xfoil (6.99.dfsg+1-3)

program for the design and analysis of subsonic airfoils

xgboost (2.0.3-1build2)

Scalable and Flexible Gradient Boosting (Executable)

xgterm (2.1+dfsg-1build2)

Terminal emulator to work with IRAF

ximtool (2.1+dfsg-1build2)

Interactive image display program for the X Window System

xmakemol (5.16-10build3)

program for visualizing atomic and molecular systems

xmakemol-gl (5.16-10build3)

program for visualizing atomic and molecular systems (OpenGL)

xmds2 (3.1.0+dfsg2-8)

eXtensible Multi-Dimensional Simulator

xmpsolve (3.2.1-10.1build4)

Multiprecision polynomial solver (graphical version)

xpa-tools (2.1.20-1build1)

Tools for seamless communication between Unix programs

xplot (1.19-9.1build1)

simple on-screen x-y column data plotter

xplot-xplot.org (0.90.7.1-4)

fast tool to graph and visualize lots of data

xpore (2.1-2)

Nanopore analysis of differential RNA modifications

xppaut (6.11b+1.dfsg-1.1)

Phase Plane Plus Auto: Solves many kinds of equations

xpython (0.15.10+~0.6.1-2build2)

Native jupyter kernel for python (binary)

xtb (6.6.1-1)

semiempirical extended tight-binding program package

xtide (2.15.2-1.1)

provides tide and current predictions

xtide-coastline (20020202-1.3)

coastline data for xtide

xtide-data (20191229-1.1)

Harmonics data for xtide

xyscan (4.64-2build3)

data thief for scientists

yagv (0.4~20171211.r234ef16+dfsg-2)

yet another G-code viewer

yaha (0.1.83-3)

find split-read mappings on single-end queries

yanagiba (1.0.0-5)

filter low quality Oxford Nanopore reads basecalled with Albacore

yanosim (0.1-5)

read simulator nanopore DRS datasets

yorick-av (0.0.6-1build2)

write movies from Yorick in various formats

yorick-full (2.2.04+dfsg1+full)

full installation of the Yorick interpreter and add-ons

yorick-gy (0.0.5-2build2)

GObject introspection and Gtk bindings for Yorick

yorick-gyoto (2.0.2-1.1build3)

General relativistic geodesic integration for the Yorick language

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

optical interferometry image reconstruction within Yorick

yorick-mpeg (0.1-4)

MPEG output support for the Yorick language

yorick-mpy-common (2.2.04+dfsg1-12build3)

Message Passing Yorick (common files)

yorick-mpy-mpich2 (2.2.04+dfsg1-12build3)

Message Passing Yorick (MPICH2 build)

yorick-mpy-openmpi (2.2.04+dfsg1-12build3)

Message Passing Yorick (OpenMPI build)

yorick-svipc (0.16-5build8)

interprocess communication (shared memory...) for Yorick

yorick-ygsl (1.2.1-1build3)

GSL special functions plugin for the Yorick language

yorick-ynfft (1.0.3-1build1)

nonequispaced fast Fourier transform for Yorick

z3 (4.8.12-3.1build1)

theorem prover from Microsoft Research

z88 (13.0.0+dfsg2-6build2)

Finite Element Analysis Program - runtime

zegrapher (3.1.1-4build2)

plotting mathematical functions and sequences on the plane

zfp (1.0.1-3.1build1)

Fixed-Rate Compressed Floating-Point Arrays - binary programs

ztex-bmp (20120314-2build1)

universal macro processor