Software Packages in "trixie", Subsection science

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
abpoa (1.5.3-1 b2)
adaptive banded Partial Order Alignment
abyss (2.3.10-1 b1)
de novo, parallel, sequence assembler for short reads
achilles (2-13)
Artificial life and evolution simulator
adapterremoval (2.3.3-3 b1 [arm64], 2.3.3-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
rapid adapter trimming, identification, and read merging of gene sequences
adapterremoval-examples (2.3.3-3)
rapid adapter trimming, identification, and read merging (example data)
adms (2.3.7-1 b2)
Automatic device model synthesizer for Verilog-AMS
adun-core (0.81-14 b8 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.81-14 b4 [riscv64])
Molecular Simulator
aegean (0.16.0 dfsg-4 b1 [arm64], 0.16.0 dfsg-4 [amd64, armel, armhf, i386, ppc64el, s390x])
integrated genome analysis toolkit
aevol (5.0 ds-4)
digital genetics model to run Evolution Experiments in silico
aghermann (1.1.2-5 b3 [riscv64], 1.1.2-5 b2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Sleep-research experiment manager
aladin (12.060 dfsg-3)
Interactive sky atlas for astronomical images and datasets
alfa (2.2-1 b3 [arm64], 2.2-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 (4.3.0-3)
NGS copy number algorithms
altree (1.3.2-2 b5 [riscv64], 1.3.2-2 b4 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
program to perform phylogeny-based association and localization analysis
altree-examples (1.3.2-2)
example files for ALTree
amap-align (2.2 git20080214.600fc29 dfsg-2 b1 [arm64, riscv64], 2.2 git20080214.600fc29 dfsg-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Protein multiple alignment by sequence annealing
ampliconnoise (1.29-15 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 1.29-15 [armel, armhf, i386])
removal of noise from 454 sequenced PCR amplicons
andi (0.14-3 b1)
Efficient Estimation of Evolutionary Distances
ants (2.4.3 dfsg-1)
advanced normalization tools for brain and image analysis
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 (3.4.0-3 b1)
Find RFI in radio astronomical observations
apbs (3.4.1-6 b1)
Adaptive Poisson Boltzmann Solver
apbs-data (3.4.1-6)
data files for APBS (Adaptive Poisson Boltzmann Solver)
apbs-doc (3.4.1-6)
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-anaphora (1.1.1-1 b2 [arm64], 1.1.1-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Anaphora resolution module for Apertium
apertium-apy (0.11.7-2.2)
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-dan-nor (1.5.0-2)
Apertium translation data for the Danish-Norwegian pair
apertium-dev (3.9.4-1 b2)
Development tools and library for Apertium
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-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-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-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-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-swe (0.1.1-2)
Apertium translation data for the Icelandic-Swedish pair
apertium-lex-tools (0.4.2-2 b4)
Constraint-based lexical selection module
apertium-lex-tools-dev (0.4.2-2 b4)
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-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 (1.1.2-1 b2 [arm64], 1.1.2-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 (0.6.1-1 b2 [arm64], 0.6.1-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Reordering separable/discontiguous multiwords
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
aragorn (1.2.41-3 b1 [arm64], 1.2.41-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
tRNA and tmRNA detection in nucleotide sequences
arb (6.0.6-8) [non-free]
phylogenetic sequence analysis suite - main program
arb-common (6.0.6-8) [non-free]
phylogenetic sequence analysis suite - common files
arden (1.0-6)
specificity control for read alignments using an artificial reference
ariba (2.14.7 ds-5)
Antibiotic Resistance Identification By Assembly
art-nextgen-simulation-tools (20160605 dfsg-5 b2 [riscv64], 20160605 dfsg-5 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
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-4)
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 (4.0.0-1)
Command line tool to manipulate ASDF scientific data files
ase (3.23.0-1)
Atomic Simulation Environment
assembly-stats (1.0.1 ds-6 b1 [riscv64], 1.0.1 ds-6 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
get assembly statistics from FASTA and FASTQ files
assemblytics (1.2.1 dfsg-2)
detect and analyze structural variants from a genome assembly
astap (2024.05.01-1)
astrometric (plate) solver, stacking of images, photometry and FITS viewer
astap-cli (2024.05.01-1)
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-2mass (1.1) [contrib]
Astrometry.net 2MASS index files downloader
astrometry-data-2mass-00 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (2'-2.8')
astrometry-data-2mass-01 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (2.8'-4')
astrometry-data-2mass-02 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (4'-5.6')
astrometry-data-2mass-03 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (5.6'-8')
astrometry-data-2mass-04 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (8'-11')
astrometry-data-2mass-05 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (11'-16')
astrometry-data-2mass-06 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (16'-22')
astrometry-data-2mass-07 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (22'-30')
astrometry-data-2mass-08-19 (1.1) [contrib]
Astrometry.net 2MASS index files downloader (30'-2000')
astrometry-data-tycho2 (2-4)
Astrometry.net Tycho-2 index files
astrometry-data-tycho2-07 (2-4 b1)
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 b1)
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 b1)
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 b1)
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 (0.97 dfsg-1)
Astrometry plate solver
astronomical-almanac (5.6-7 b1 [riscv64], 5.6-7 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
astronomical almanac - calculate planet and star positions
astropy-utils (7.0.0-1)
Command line tools from astropy
atac (0~20150903 r2013-9)
genome assembly-to-assembly comparison
ataqv (1.3.1 ds-2 b3 [arm64], 1.3.1 ds-2 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64])
ATAC-seq QC and visualization
atomes (1.1.15-1)
atomic-scale 3D modeling toolbox
atomes-data (1.1.15-1)
atomic-scale 3D modeling toolbox (data)
atropos (1.1.32 dfsg-2 b1)
NGS read trimming tool that is specific, sensitive, and speedy
augur (24.4.0-1)
pipeline components for real-time virus analysis
augustus (3.5.0 dfsg-4 b6 [riscv64], 3.5.0 dfsg-4 b5 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
gene prediction in eukaryotic genomes
augustus-data (3.5.0 dfsg-4)
data files for AUGUSTUS
autodock (4.2.6-9 b1 [arm64, riscv64], 4.2.6-9 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (1.2.5-2 b1 [arm64], 1.2.5-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
docking of small molecules to proteins
autogrid (4.2.6-9 b1 [arm64, riscv64], 4.2.6-9 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
pre-calculate binding of ligands to their receptor
autogrid-test (4.2.6-9)
test files for AutoGrid
avce00 (2.0.0-9 b1 [arm64, riscv64], 2.0.0-9 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Conversion of ESRI Arcinfo Vector Coverage in E00 format
avogadro (1.99.0-1 b2 [arm64], 1.99.0-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Molecular Graphics and Modelling System
avogadro-utils (1.99.0-5 b4)
Molecular Graphics and Modelling System (library)
axe-demultiplexer (0.3.3 dfsg-4 b1)
Trie-based DNA sequencing read demultiplexer
bagel (1.2.2-8)
Computational Chemistry Package
baitfisher (1.2.7 git20211020.de26d5c dfsg-2)
software package for designing hybrid enrichment probes
bali-phy (3.6.1 dfsg-3)
Bayesian Inference of Alignment and Phylogeny
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-6 b1)
toolkit for manipulating BAM (genome alignment) files
bandage (0.9.0-2 b3 [riscv64], 0.9.0-2 b2 [arm64], 0.9.0-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Bioinformatics Application for Navigating De novo Assembly Graphs Easily
bandage-examples (0.9.0-2)
Bioinformatics Application for Navigating De novo Assembly Graphs Easily (data)
barrnap (0.9 dfsg-4)
rapid ribosomal RNA prediction
bart (0.9.00-3)
tools for computational magnetic resonance imaging
bart-view (0.3.00-1 b2 [arm64], 0.3.00-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
viewer for multi-dimensional complex-valued data
bbmap (39.13 dfsg-1)
BBTools genomic aligner and other tools for short sequences
bbmap-jni (39.13 dfsg-1)
short read aligner and other bioinformatic tools - JNI library
bcalm (2.2.3-5 b3 [arm64], 2.2.3-5 b2 [amd64, mips64el, ppc64el, riscv64])
de Bruijn compaction in low memory
bcftools (1.20-2 b1 [arm64], 1.20-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
genomic variant calling and manipulation of VCF/BCF files
beads (1.1.22-1 b4 [arm64, armel, armhf, riscv64], 1.1.22-1 b3 [amd64, i386, mips64el, ppc64el, s390x])
2-DE electrophoresis gel image spot detection
beagle (241029-1)
Genotype calling, genotype phasing and imputation of ungenotyped markers
beast-mcmc (1.10.4 dfsg-5)
Bayesian MCMC phylogenetic inference
beast2-mcmc (2.7.6 dfsg-1)
Bayesian MCMC phylogenetic inference
bedops (2.4.41 dfsg-3)
high-performance genomic feature operations
bedtools (2.31.1 dfsg-2 b2 [riscv64], 2.31.1 dfsg-2 b1 [arm64], 2.31.1 dfsg-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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-7.1 b2)
multiple sequence alignment viewer and phylogenetic tool
berkeley-express (1.5.3 dfsg-3 b4 [arm64], 1.5.3 dfsg-3 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.5.3 dfsg-3 b2 [riscv64])
Streaming quantification for high-throughput sequencing
bio-eagle (2.4.1-3 b3)
Haplotype phasing within a genotyped cohort or using a phased reference panel
bio-eagle-examples (2.4.1-3)
Examples for bio-eagle
bio-rainbow (2.0.4 dfsg-2 b2 [riscv64], 2.0.4 dfsg-2 b1 [arm64], 2.0.4 dfsg-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
clustering and assembling short reads for bioinformatics
bio-vcf (0.9.5-3)
domain specific language (DSL) for processing the VCF format
bioawk (1.0-5 b1 [arm64], 1.0-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
extension of awk for biological sequence analysis
biobambam2 (2.0.185 ds-2)
tools for early stage alignment file processing
biogenesis (0.8-3.2)
artificial life program that simulates evolution of organisms
bioperl (1.7.8-1)
Perl tools for computational molecular biology
bioperl-run (1.7.3-13)
BioPerl wrappers: scripts
biosig-tools (2.6.1-1 b1)
format conversion tools for biomedical data formats
biosquid (1.9g cvs20050121-15.1 b1)
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 b2 [riscv64], 0.7.5 dfsg-6 b1 [arm64], 0.7.5 dfsg-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Bayesian Inference of Transcripts from Sequencing Data
bitwise (0.50-1 b2 [arm64], 0.50-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Interactive bitwise operation in ncurses
bkchem (0.14.0~pre4 git20211228-5)
Chemical structures editor
blasr (5.3.5 dfsg-6 b3 [amd64, arm64, mips64el, ppc64el], 5.3.5 dfsg-6 b1 [riscv64])
mapping single-molecule sequencing reads
blimps-utils (3.9 ds-3) [non-free]
blocks database improved searcher
blixem (4.44.1 dfsg-7.1 b2)
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 b2 [riscv64], 1.5.118.6b56be4.121013-1.3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
SMT solver for bit-vectors and arrays
bornagain (22~git20240726093306.cb41cc4 ds3-2)
Simulate and fit X-ray and neutron GISAS -- binary
bowtie (1.3.1-3 b1 [arm64], 1.3.1-3 [amd64, mips64el, ppc64el, riscv64, s390x])
Ultrafast memory-efficient short read aligner
bowtie-examples (1.3.1-3)
Examples for bowtie, the ultrafast memory-efficient short read aligner
bowtie2 (2.5.4-1 b1 [amd64, arm64, mips64el, ppc64el], 2.5.4-1 [riscv64])
ultrafast memory-efficient short read aligner
bowtie2-examples (2.5.4-1)
Examples for bowtie2
boxshade (3.3.1-14 b2 [riscv64], 3.3.1-14 b1 [arm64], 3.3.1-14 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Pretty-printing of multiple sequence alignments
bppphyview (0.6.1-5 b1 [arm64], 0.6.1-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Bio Phylogenetic Viewer
bppsuite (2.4.1-7 b1 [arm64], 2.4.1-7 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Bio program suite
bppsuite-examples (2.4.1-7)
Examples for Bio program suite
brain2mesh-demos (0.7.9-3)
sample files and demo scripts for Brain2Mesh
brig (0.95 dfsg-3 b2 [riscv64], 0.95 dfsg-3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
BLAST Ring Image Generator
btllib-tools (1.4.10 dfsg-1 b2 [riscv64], 1.4.10 dfsg-1 b1 [arm64], 1.4.10 dfsg-1 [amd64, mips64el, ppc64el])
Bioinformatics Technology Lab common code library tools
busco (5.5.0-3)
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 (0.7.18-1)
Burrows-Wheeler Aligner
c-munipack (2.1.37-1 b1 [arm64], 2.1.37-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
reduction of images carried out by CCD camera
c-munipack-share (2.1.37-1)
reduction of images carried out by CCD camera (share)
c2x (2.41.b ds-2)
converter between DFT electronic structure codes formats
calceph (4.0.3-1)
Planetary ephemeris data access tools
callisto (1.1.0-3 b1 [arm64], 1.1.0-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Daemon for e-Callisto hardware
camitk-actionstatemachine (5.2.0-2 b4)
pipeline replay application for the CamiTK library
camitk-config (5.2.0-2 b4)
Computer Assisted Medical Intervention Tool Kit - config
camitk-imp (5.2.0-2 b4)
workbench application for the CamiTK library
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 git2018.12.08-3)
Table of radio observatory coordinates for casacore
casacore-data-sources (2-6)
Table of ICRF reference source coordinates for casacore
casacore-data-tai-utc (1.3)
Difference table between TAI and UTC for casacore
casacore-tools (3.6.1-3)
Tools built with CASA
cassbeam (1.1-4 b2 [arm64, riscv64], 1.1-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Cassegrain antenna modelling
cassiopee (1.0.9-4 b2 [arm64], 1.0.9-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 (0.3.6-6 b5 [mips64el], 0.3.6-6 b4 [amd64, arm64, armel, armhf, i386, ppc64el, s390x], 0.3.6-6 b3 [riscv64])
Continuous Beam Analysis
cbflib-bin (0.9.7 dfsg1-4 b2)
utilities to manipulate CBF files
cbmc (6.1.1-2)
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 b1 [arm64, riscv64], 4.8.1-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
suite of programs designed to quickly group sequences
cdbfasta (1.00 git20230710.da8f5ba dfsg-1 b1 [arm64, riscv64], 1.00 git20230710.da8f5ba dfsg-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Constant DataBase indexing and retrieval tools for multi-FASTA files
centrifuge (1.0.4.2-1)
rapid and memory-efficient system for classification of DNA sequences
cg3 (1.4.6-1 b3)
Tools for using the 3rd edition of Constraint Grammar (CG-3)
cg3-dev (1.4.6-1)
Metapackage providing both CG-3 CLI dev tools and dev library
cgns-convert (3.4.0-5 b1)
CFD General Notation System - Conversion tools
cgview (0.0.20100111-7)
Circular Genome Viewer
ch5m3d (1.2.5 dfsg-3)
create and visualize 3-dimensional drawings of simple molecules
changeo (1.3.0-3)
Repertoire clonal assignment toolkit (Python 3)
checkit-tiff (1.4.4-2)
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 (0.10.0-1)
derive IUPAC systematic names for chemical structures
chemtool (1.6.14-6 b2 [arm64, riscv64], 1.6.14-6 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
chemical structures drawing program
chimeraslayer (20101212 dfsg1-6)
detects likely chimeras in PCR amplified DNA
chip-seq (1.5.5-3 b1 [arm64, riscv64], 1.5.5-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (0.4.2-5 b2)
transform CIF data among CIF formats and dialects
cif-tools (1.0.12-4)
Suite of tools to manipulate, validate and query mmCIF files
cif2hkl (1.4.5 ds1-1)
Convert crystallographic descriptions into HKL F^2 reflection lists
circos (0.69.9 dfsg-2)
plotter for visualizing data
circos-tools (0.23-1)
plotter for visualizing data - helper utilities
ckon (0.7.1-5 b5 [arm64], 0.7.1-5 b4 [amd64, armel, armhf, i386, mips64el, ppc64el], 0.7.1-5 b3 [riscv64, s390x])
automatic build tool for ROOT data analysis software
clearcut (1.0.9 git20211013.b799afe-1 b1 [arm64, riscv64], 1.0.9 git20211013.b799afe-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
extremely efficient phylogenetic tree reconstruction
clonalframe (1.2-11 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.2-11 b2 [riscv64])
inference of bacterial microevolution using multilocus sequence data
clonalframeml (1.13-1 b1 [arm64], 1.13-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Efficient Inference of Recombination in Whole Bacterial Genomes
clonalorigin (1.0-8 b1)
inference of homologous recombination in bacteria using whole genome sequences
clustalo (1.2.4-8 b1 [arm64], 1.2.4-8 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
General-purpose multiple sequence alignment program for proteins
clustalw (2.1 lgpl-7 b1 [arm64, riscv64], 2.1 lgpl-7 [amd64, mips64el, ppc64el, s390x])
global multiple nucleotide or peptide sequence alignment
clustalx (2.1 lgpl-9 b2 [arm64, riscv64], 2.1 lgpl-9 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Multiple alignment of nucleic acid and protein sequences (graphical interface)
cluster3 (1.59 ds-6) [non-free]
Reimplementation of the Eisen-clustering software
cmor-tables (3.3-1.1)
MIP tables for the Climate Model Output Rewriter library
cnvkit (0.9.10-2)
Copy number variant detection from targeted DNA sequencing
cod-tools (3.10.0 dfsg-2 b2)
tools for manipulating CIF format files
codonw (1.4.4-8 b1 [arm64], 1.4.4-8 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Correspondence Analysis of Codon Usage
coinor-cbc (2.10.12 ds-1)
Coin-or branch-and-cut mixed integer programming solver
coinor-clp (1.17.10 ds-1)
Coin-or linear programming solver
coinor-csdp (6.2.0-5 b2)
Software package for semidefinite programming (binaries)
coinor-libbonmin4t64 (1.8.9-1.1 b2)
COIN-OR mixed integer programming
coinor-libcbc3.1 (2.10.12 ds-1)
Coin-or branch-and-cut mixed integer programming solver (shared libraries)
coinor-libcgl1 (0.60.9 ds-1)
COIN-OR Cut Generation Library
coinor-libclp1 (1.17.10 ds-1)
Coin-or linear programming solver (shared libraries)
coinor-libcoinutils3v5 (2.11.11 ds-2)
COIN-OR collection of utility classes (shared libraries)
coinor-libosi1v5 (0.108.10 ds-1 b1)
COIN-OR Open Solver Interface
coinor-libvol1 (1.5.4-4 b1 [arm64, riscv64], 1.5.4-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Coin-or linear programming solver (libraries)
colmap (3.10-1 b1 [arm64], 3.10-1 [amd64, i386, mips64el, ppc64el, riscv64, s390x])
Structure-from-Motion and Multi-View Stereo
comet-ms (2019015 cleaned1-4.1 b1 [arm64], 2019015 cleaned1-4.1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Tandem mass spectrometry (MS/MS) search engine
concavity (0.1 dfsg.1-6)
predictor of protein ligand binding sites from structure and conservation
conda-package-handling (2.3.0-1)
create and extract conda packages of various formats
condor (23.6.2 dfsg-2)
distributed workload management system
condor-annex-ec2 (23.6.2 dfsg-2)
distributed workload management system - single node configuration
condor-kbdd (23.6.2 dfsg-2)
distributed workload management system - single node configuration
condor-test (23.6.2 dfsg-2)
distributed workload management system - single node configuration
condor-upgrade-checks (23.6.2 dfsg-2)
distributed workload management system - single node configuration
condor-vm-gahp (23.6.2 dfsg-2)
distributed workload management system - single node configuration
connectome-workbench (2.0.1-1)
brain visualization, analysis and discovery tool
conservation-code (20110309.0-8)
protein sequence conservation scoring tool
covtobed (1.3.5 dfsg-2 b1 [arm64, riscv64], 1.3.5 dfsg-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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
cpptraj (5.1.0 dfsg-4)
fast, parallelized molecular dynamics trajectory data analysis
cpuinfo (0.0~git20240830.fa1c679-5)
CPU INFOrmation library (binary utilities)
crac (2.5.2 dfsg-6 b1 [arm64, mips64el, ppc64el, riscv64], 2.5.2 dfsg-6 [amd64])
integrated RNA-Seq read analysis
critterding (1.0-beta12.1 dfsg-1)
Evolving Artificial Life
ctdconverter (2.1-8)
Convert CTD files into Galaxy tool and CWL CommandLineTool files
ctffind (4.1.14-3 b1 [arm64], 4.1.14-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
fast and accurate defocus estimation from electron micrographs
ctsim (6.0.2-6 b6 [mips64el], 6.0.2-6 b5 [amd64, arm64, armel, armhf, i386, ppc64el, s390x], 6.0.2-6 b4 [riscv64])
Computed tomography simulator
ctsim-help (6.0.2-6)
Online help file for CTSim
cufflinks (2.2.1 dfsg.1-10) [non-free]
Transcript assembly, differential expression and regulation for RNA-Seq
cutadapt (4.7-2)
Clean biological sequences from high-throughput sequencing reads
cutesv (2.1.1-1)
comprehensive discovery of structural variations of genomic sequences
cwl-upgrader (1.2.11-1)
Common Workflow Language standalone document upgrader
cwlformat (2022.02.18-3)
code formatter for Common Workflow Language
cwltest (2.5.20241122133319-1)
Common Workflow Language testing framework
cwltool (3.1.20241112140730-1)
Common Workflow Language reference implementation
cwltool-doc (3.1.20241112140730-1)
Common Workflow Language reference implementation -- docs
daligner (1.0 git20240119.335105d-3 b1 [arm64], 1.0 git20240119.335105d-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
local alignment discovery between long nucleotide sequencing reads
damapper (0.0 git20240314.b025cf9-1)
long read to reference genome mapping tool
darknet (0.0.0 git20180914.61c9d02e-3)
Open Source Neural Networks in C
dascrubber (1.1-4 b1 [arm64, riscv64], 1.1-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
alignment-based scrubbing pipeline for DNA sequencing reads
datalad (1.1.4-1)
data files management and distribution platform
datalad-container (1.2.5-1)
DataLad extension for working with containerized environments
dawg (1.2-4 b2 [arm64], 1.2-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
simulate the evolution of recombinant DNA sequences
dazzdb (1.0 git20240115.be65e59-1 b1 [arm64], 1.0 git20240115.be65e59-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
manage nucleotide sequencing read data
dcl-f77 (7.5.1-2)
GFD-DENNOU Club Library (DCL) - FORTRAN77 version
dcm2niix (1.0.20240202-1)
next generation DICOM to NIfTI converter
dcmtk (3.6.8-6 b1)
OFFIS DICOM toolkit command line utilities
dcmtk-data (3.6.8-6)
OFFIS DICOM toolkit data files
(4.1)
Debian Astronomy Pure Blends Logo
deblur (1.1.1-3)
deconvolution for Illumina amplicon sequencing
delly (1.1.8-1 b3 [arm64], 1.1.8-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Structural variant discovery by read analysis
density-fitness (1.0.12-2)
Calculates per-residue electron density scores
dextractor (1.0-6 b3 [riscv64], 1.0-6 b2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
(d)extractor and compression command library
dh-r (20241218)
Debian helper tools for packaging R libraries
dialign (2.2.1-13 b1 [arm64], 2.2.1-13 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Segment-based multiple sequence alignment
dialign-tx (1.0.2-15 b1 [arm64], 1.0.2-15 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Segment-based multiple sequence alignment
dialign-tx-data (1.0.2-15)
Segment-based multiple sequence alignment (data files)
dials (3.22.1 dfsg3-1)
Diffraction Integration for Advanced Light Sources
diamond-aligner (2.1.9-1)
accelerated BLAST compatible local sequence aligner
dimbl (0.17-2 b1 [arm64], 0.17-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Distributed Memory Based Learner
discosnp (1:2.6.2-4 b1)
discovering Single Nucleotide Polymorphism from raw set(s) of reads
disulfinder (1.2.11-12 b1 [arm64, riscv64], 1.2.11-12 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (6.06-2 b1)
Density matrix renormalization group algorithm
dnaclust (3-7 b4 [arm64], 3-7 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 3-7 b1 [riscv64])
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
doris (5.0.3~beta dfsg-17) [contrib]
Delft object-oriented radar interferometric software
dotter (4.44.1 dfsg-7.1 b2)
detailed comparison of two genomic sequences
dozzaqueux (3.51-4)
simulator for chemical mixtures
dozzaqueux-data (3.51-4)
databases for chemical mixtures
dpuser (4.2 dfsg-1)
Interactive language for handling numbers, strings, and matrices
drat-trim (0.0~git20240428.effa1dc-2)
DART-trim satisfiability proof checker (binary utils)
drat-trim-examples (0.0~git20240428.effa1dc-2)
DART-trim satisfiability proof checker (example files)
drawxtl (5.5-6.1 b2 [arm64, riscv64], 5.5-6.1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
crystal structure viewer
drop-seq-testdata (3.0.2 dfsg-1)
analyzing Drop-seq data (testdata)
drop-seq-tools (3.0.2 dfsg-1)
analyzing Drop-seq data
drs4eb (5.0.6 git20211217 ds-4 b1 [arm64], 5.0.6 git20211217 ds-4 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
DRS4 Evaluation Board software
drslib (0.3.2-1)
Command-line tools for the Data Reference Syntax library
dsdp (5.8-10.1)
Software for Semidefinite Programming
dssp (4.4.10-1)
protein secondary structure assignment based on 3D structure
dwgsim (0.1.14-3)
short sequencing read simulator
dx (1:4.4.4-18)
OpenDX (IBM Visualization Data Explorer) - main package
dxf2gcode (20240509-2)
prepares drawings of parts for automatic machine tools
dxsamples (4.4.0-5)
Sample programs for the OpenDX Data Explorer
e-mem (1.0.1-5 b1 [arm64, riscv64], 1.0.1-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Efficient computation of Maximal Exact Matches for very large genomes
e00compr (1.0.1-7 b1 [arm64, riscv64], 1.0.1-7 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Program to read/write Arcinfo compressed E00 files
ea-utils (1.1.2 dfsg-9 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.1.2 dfsg-9 b2 [riscv64])
command-line tools for processing biological sequencing data
easychem (0.6-9 b2 [arm64, riscv64], 0.6-9 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Draw high-quality molecules and 2D chemical formulas
ecaccess (4.0.1-1.1)
clients to access ECMWF facilities
ecflow-client (5.13.6-1)
Client tools for Meteorological workflow
ecflow-server (5.13.6-1)
Meteorological workflow controller - server
ecopcr (1.0.1 dfsg-5 b1 [arm64], 1.0.1 dfsg-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
estimate PCR barcode primers quality
ectrans-utils (1.5.0-3)
Spherical Harmonics Transforms library - utilities
edfbrowser (2.12 dfsg-1)
viewer for biosignal storage files such as bdf and edf
edlib-aligner (1.2.7-6 b2)
edlib sequence alignment tool using edit distance
edtsurf (0.2009-10 b1 [arm64, riscv64], 0.2009-10 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
triangulated mesh surfaces for protein structures
eigensoft (8.0.0 dfsg-2 b1)
reduction of population bias for genetic analyses
elastix (5.1.0-1)
toolbox for rigid and nonrigid registration of images
elk-lapw (9.6.8-1 b1)
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 b1 [arm64, riscv64], 1.0.1-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
DNA/protein sequence motif finder
embassy-domainatrix (0.1.660-5 b1 [arm64], 0.1.660-5 [amd64, mips64el, ppc64el, riscv64])
Extra EMBOSS commands to handle domain classification file
embassy-domalign (0.1.660-5 b1 [arm64], 0.1.660-5 [amd64, mips64el, ppc64el, riscv64])
Extra EMBOSS commands for protein domain alignment
embassy-domsearch (1:0.1.660-4 b1 [arm64], 1:0.1.660-4 [amd64, mips64el, ppc64el, riscv64])
Extra EMBOSS commands to search for protein domains
emboss (6.6.0 dfsg-15 b1 [arm64], 6.6.0 dfsg-15 [amd64, mips64el, ppc64el, riscv64])
European molecular biology open software suite
emboss-data (6.6.0 dfsg-15)
data files for the EMBOSS package
emboss-explorer (2.2.0-12)
web-based GUI to EMBOSS
emboss-lib (6.6.0 dfsg-15 b1 [arm64], 6.6.0 dfsg-15 [amd64, mips64el, ppc64el, riscv64])
EMBOSS Libraries
emmax (0~beta.20100307-5 b1 [arm64, riscv64], 0~beta.20100307-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
genetic mapping considering population structure
engauge-digitizer (12.1 ds.1-1 b2 [arm64, riscv64], 12.1 ds.1-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
interactively extracts numbers from bitmap graphs or maps
ent (1.2debian-3 b1 [arm64, riscv64], 1.2debian-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
pseudorandom number sequence test program
epics-base (7.0.8.1 dfsg1-6)
EPICS tools
ergo (3.8.2-1.1)
Quantum chemistry program for large-scale calculations
ergo-data (3.8.2-1.1)
Quantum chemistry program for large-scale calculations - data package
eso-midas (23.02pl1.0-3)
European Southern Observatory Munich Image Data Analysis System
eso-midas-testdata (23.02pl1.0-3)
Test data files for ESO-MIDAS
esorex (3.13.7 ds-1 b1 [arm64, riscv64], 3.13.7 ds-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Execution Tool for European Southern Observatory pipelines
estscan (3.0.3-6 b1 [arm64, riscv64], 3.0.3-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
ORF-independent detector of coding DNA sequences
etsf-io (1.0.4-5 b2 [arm64, riscv64], 1.0.4-5 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Binary tools to check, merge and read ETSF files
examl (3.0.22-6 b2 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 3.0.22-6 b1 [armel, armhf, i386])
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
exonerate (2.4.0-5 b2 [arm64, riscv64], 2.4.0-5 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
generic tool for pairwise sequence comparison
expeyes (5.3.3 repack-1)
hardware & software framework for developing science experiments
expeyes-clib (5.3.3 repack-1)
hardware & software framework for developing science experiments
eye (22.1201.1601~ds-1)
semantic web reasoning engine
eyes17 (5.3.3 repack-1)
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 (0.6.5-8)
utilities for manipulating Oxford Nanopore Fast5 files
fasta3 (36.3.8i.14-Nov-2020-3)
tools for searching collections of biological sequences
fastahack (1.0.0 dfsg-11 b2)
utility for indexing and sequence extraction from FASTA files
fastani (1.33-3 b2 [riscv64], 1.33-3 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Fast alignment-free computation of whole-genome Average Nucleotide Identity
fastaq (3.17.0-9)
FASTA and FASTQ file manipulation tools
fastdnaml (1.2.2-17 b1 [arm64], 1.2.2-17 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Tool for construction of phylogenetic trees of DNA sequences
fastlink (4.1P-fix100 dfsg-5 b1 [arm64], 4.1P-fix100 dfsg-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
faster version of pedigree programs of Linkage
fastml (3.11-4 b1 [arm64], 3.11-4 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
maximum likelihood ancestral amino-acid sequence reconstruction
fastp (0.23.4 dfsg-1 b1 [arm64, riscv64], 0.23.4 dfsg-1 [amd64, armel, armhf, mips64el, ppc64el, s390x])
Ultra-fast all-in-one FASTQ preprocessor
fastq-pair (1.0-3 b1 [arm64, riscv64], 1.0-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Rewrites paired end fastq so all reads have a mate to separate out singletons
fastqc (0.12.1 dfsg-4)
quality control for high throughput sequence data
fastqtl (2.184 v7 dfsg-4 b3)
Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
fasttext (0.9.2 ds-7 b3)
Efficient learning of word representations and sentence classification library
fasttree (2.1.11-2 b1 [arm64, riscv64], 2.1.11-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
phylogenetic trees from alignments of nucleotide or protein sequences
fcc (2.16-1 b1 [riscv64], 2.16-1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [riscv64], 0.2 dfsg-2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Open Source theoretical EXAFS calculations
ffindex (0.9.9.9-7 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 0.9.9.9-7 [armel, armhf, i386])
simple index/database for huge amounts of small files
fiat-utils (1.4.1-1 b1)
Fortran IFS and Arpege Toolkit - utilities
figtree (1.4.4-6)
graphical phylogenetic tree viewer
filtlong (0.2.1-4 b1 [arm64, riscv64], 0.2.1-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (137 dfsg-2)
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 (1.4.4-6 b1 [arm64], 1.4.4-6 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Extract cutouts from FITS image format files
fitsh (0.9.4-1 b1 [arm64, riscv64], 0.9.4-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Software package for astronomical image processing
fitspng (2.0-2 b2 [arm64], 2.0-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
FITS to PNG converter
fitsverify (4.22 cfitsio4.5.0-5)
transitional dummy package
fitsverify
virtual package provided by libcfitsio-bin
fityk (1.3.2-3 b5 [arm64, armhf, mips64el, riscv64], 1.3.2-3 b4 [amd64, armel, i386, ppc64el, s390x])
general-purpose nonlinear curve fitting and data analysis
flash (1.2.11-2 b1 [arm64, riscv64], 1.2.11-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Fast Length Adjustment of SHort reads
flexbar (1:3.5.0-5 b1 [arm64, riscv64], 1:3.5.0-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
flexible barcode and adapter removal for sequencing platforms
flextra (5.0-17 b1 [riscv64], 5.0-17 [amd64, arm64, mips64el, ppc64el])
Trajectory model for tracing air transport phenomena
flye (2.9.5 dfsg-1)
de novo assembler for single molecule sequencing reads using repeat graphs
fml-asm (0.1 git20221215.85f159e-1)
tool for assembling Illumina short reads in small regions
foma (1:0.10.0 s311.20240712-1)
Tools for constructing various finite-state automata
form (4.3.1 git20240409 ds-2 b1)
Symbolic manipulation system
fractalnow (0.8.2-5 b2 [arm64, riscv64], 0.8.2-5 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Fast, advanced fractal generator
(3.1.10 ds-1)
Free42 is a re-implementation of the HP-42S calculator
freecad (0.21.2 dfsg1-6)
Extensible Open Source CAx program
freecad-common (0.21.2 dfsg1-6)
Extensible Open Source CAx program - common files
freecad-python3 (0.21.2 dfsg1-6 b1)
Extensible Open Source CAx program - Python 3 binaries
freecontact (1.0.21-14)
fast protein contact predictor
freesasa (2.1.2-4 b1 [arm64, riscv64], 2.1.2-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Solvent Accessible Surface Area of biomolecules
frog (0.32-2 b1)
tagger and parser for natural languages (runtime)
frogdata (0.22-1)
Data files for Frog
fsa (1.15.9 dfsg-6 b1 [arm64, riscv64], 1.15.9 dfsg-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Fast Statistical Alignment of protein, RNA or DNA sequences
fsm-lite (1.0-8 b1 [arm64, riscv64], 1.0-8 [amd64, mips64el, ppc64el, s390x])
frequency-based string mining (lite)
ftools-fv (5.5.3 dfsg-1)
Tool for viewing and editing FITS format files
ftools-pow (5.5.3 dfsg-1 b1)
Curve plotting and image display interface tool
funtools (1.4.8-1.1 b2)
Minimal buy-in FITS utility package
fxt-tools (0.3.13-4.1 b1)
Multithreaded tracing library
galileo (0.5.1-11)
Utility to securely synchronize a Fitbit device with the Fitbit web service
galileo-daemon (0.5.1-11)
Utility to securely synchronize a Fitbit device - daemon
galvani (0.38-1)
reads data from a device with graphical plots and evaluation
garlic (1.6-3 b1 [amd64, arm64, riscv64], 1.6-3 [armel, armhf, i386, mips64el, ppc64el, s390x])
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-13 b3)
Genome Analysis Toolbox with de-Bruijn graph
gatb-core-testdata (1.4.2 dfsg-13)
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-12)
GMOD Generic Genome Browser
gbrowse-calign (2.56 dfsg-12 b3)
CAlign helper
gbrowse-data (2.56 dfsg-12)
Sample data to use GBrowse
gbutils (6.3-1 b2 [riscv64], 6.3-1 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
utilities for command line econometrics
gdal-bin (3.9.3 dfsg-1 b2)
Geospatial Data Abstraction Library - Utility programs
gdal-data (3.9.3 dfsg-1)
Geospatial Data Abstraction Library - Data files
gdal-plugins (3.9.3 dfsg-1 b2)
Geospatial Data Abstraction Library - Plugins
gdl-astrolib (2022.09.12 dfsg-2)
Low-level astronomy software for GDL
gdl-mpfit (1.85 2017.01.03-4)
Robust non-linear least squares curve fitting for GDL
gdpc (2.2.5-16 b2 [arm64, riscv64], 2.2.5-16 b1 [amd64, mips64el, ppc64el])
visualiser of molecular dynamic simulations
gdpc-examples (2.2.5-16)
example files for the gdpc program
gelemental (2.0.2-1.1 b2)
Periodic Table viewer
gemma (0.98.5 dfsg-3)
Genome-wide Efficient Mixed Model Association
gemma-doc (0.98.5 dfsg-3)
Example folder for GEMMA
gemmi (0.6.5 ds-2 b1 [arm64], 0.6.5 ds-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
library for structural biology - executable
genometester (4.0 git20200511.91cecb5 dfsg-1 b1 [arm64, riscv64], 4.0 git20200511.91cecb5 dfsg-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
toolkit for performing set operations on k-mer lists
genomethreader (1.7.3 dfsg-10 b2 [arm64, mips64el], 1.7.3 dfsg-10 b1 [amd64, armel, armhf, i386, ppc64el, riscv64, s390x])
software tool to compute gene structure predictions
genometools (1.6.5 ds-2.2)
versatile genome analysis toolkit
genometools-common (1.6.5 ds-2.2)
shared data files for GenomeTools
gentle (1.9.5~alpha2 dfsg1-2)
suite for molecular cloning and sequence analysis
geographiclib-tools (2.4-1 b1)
C library to solve some geodesic problems -- tools
geotiff-bin (1.7.3-1 b1)
GeoTIFF (geografic enabled TIFF) library -- tools
gerris (20131206 dfsg-21 b1)
Fluid Flow Solver
getdata (0.2-4)
management of external databases
gff2aplot (2.0-15 b1 [arm64], 2.0-15 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
pair-wise alignment-plots for genomic sequences in PostScript
gff2ps (0.98l-6)
produces PostScript graphical output from GFF-files
gffread (0.12.7-8)
GFF/GTF format conversions, region filtering, FASTA sequence extraction
gfsview-batch (20121130 dfsg-8.1 b4)
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 b1 [riscv64], 1.0.7-2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Common gFTL containers of Fortran intrinsic types
ggd-utils (1.0.0 ds-1 b12 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.0.0 ds-1 b7 [riscv64])
programs for use in ggd
ghkl (5.1.2-2)
diffractometer computation control application
ghmm (0.9~rc3-10)
General Hidden-Markov-Model library - tools
ginga (5.2.0-1)
Astronomical image viewer
gjh-asl-json (0.0 git20210628.867c5da-1 b1 [arm64, riscv64], 0.0 git20210628.867c5da-1 [amd64, mips64el, ppc64el, s390x])
gjh solver, like solver from AMPL Library
glam2 (1064-10)
gapped protein motifs from unaligned sequences
glgrib-data (1.0-4)
Display GRIB2 fields using OpenGL (data for glgrib)
glgrib-egl (1.0-4 b2)
Render geophysical fields encoded in GRIB edition 2 using OpenGL
glgrib-glfw (1.0-4 b2)
Interactive display for geophysical fields encoded in GRIB2
glgrib-shaders (1.0-4)
Display GRIB2 fields using OpenGL (shaders for glgrib)
glgrib-testdata (1.0-4)
Display GRIB2 fields using OpenGL (test data for glgrib)
glgrib-tk (1.0-4 b2)
Display GRIB2 fields using OpenGL (Perl/Tk interface)
gliese (3.0.95-3) [non-free]
stellar data set from the Third Catalogue of Nearby Stars
glueviz (1.17.1 dfsg-2)
Linked data visualization
gmap (2024-11-20 ds-1)
spliced and SNP-tolerant alignment for mRNA and short reads
gmt (6.5.0 dfsg-3 b2)
Generic Mapping Tools
gmt-common (6.5.0 dfsg-3)
Generic Mapping Tools - Architecture-independent files
gmt-dcw (2.2.0-1)
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
gmtsar (6.5 ds-2)
InSAR processing system based on Generic Mapping Tools - metapackage
gmtsar-core (6.5 ds-2 b2 [arm64], 6.5 ds-2 b1 [amd64, i386, ppc64el, s390x])
InSAR processing system based on Generic Mapping Tools - core
gmtsar-data (6.5 ds-2)
InSAR processing system based on Generic Mapping Tools - data
gmtsar-scripts (6.5 ds-2)
InSAR processing system based on Generic Mapping Tools - scripts
gnuastro (0.23-2 b1)
GNU Astronomy Utilities programs
goby-java (3.3.1 dfsg2-11)
next-generation sequencing data and results analysis tool
gpaw-data (24.1.0-1)
gpaw datasets/setups
gperiodic (3.0.3-2)
periodic table application
gpx (2.6.8-1 b1 [arm64, riscv64], 2.6.8-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Gcode to x3g conversion post processor
grabix (0.1.7-5)
wee tool for random access into BGZF files
graphlan (1.1.3-6)
circular representations of taxonomic and phylogenetic trees
grass (8.4.0-1)
Geographic Resources Analysis Support System (GRASS GIS)
grass-core (8.4.0-1)
GRASS GIS core components
grass-gui (8.4.0-1)
GRASS GIS graphical user interfaces
gravit (0.5.1 dfsg-6 b2 [arm64, riscv64], 0.5.1 dfsg-6 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
visually stunning gravity simulator
gravit-data (0.5.1 dfsg-6)
data files for Gravit
gri (2.12.27-1.2)
a language for scientific illustration
grinder (0.5.4-6)
Versatile omics shotgun and amplicon sequencing read simulator
gromacs (2024.4-1 b1)
Molecular dynamics simulator, with building and analysis tools
gromacs-data (2024.4-1)
GROMACS molecular dynamics sim, data and documentation
groops (0 git20240830 ds-1 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 0 git20240830 ds-1 [armhf, i386]) [non-free]
software toolkit for gravity field recovery and GNSS processing
groops-gui (0 git20240830 ds-1 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 0 git20240830 ds-1 [armhf, i386]) [non-free]
software toolkit for gravity field recovery and GNSS processing (GUI)
gsort (0.1.4-3 b18 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.1.4-3 b7 [riscv64])
sort genomic data
gubbins (3.4-1)
phylogenetic analysis of genome sequences
gvb (1.4-1.1)
visual simulator of 1 and 2-dimensional vibrations
gwama (2.2.2 dfsg-6)
Genome-Wide Association Meta Analysis
gwyddion (2.67-1)
Scanning Probe Microscopy visualization and analysis tool
gwyddion-common (2.67-1)
architecture-independent files for Gwyddion SPM analysis tool
gyoto (2.0.2-5)
General relativistic geodesic integration and ray-tracing
gyoto-bin (2.0.2-5)
General relativistic ray-tracing command-line interface
h5utils (1.13.2-1 b3 [arm64, riscv64], 1.13.2-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
HDF5 files visualization tools
harminv (1.4.2-1 b1 [arm64, riscv64], 1.4.2-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
extraction of complex frequencies and amplitudes from time series
harvest-tools (1.3-8 b6 [armel, armhf], 1.3-8 b5 [arm64], 1.3-8 b4 [amd64, i386, mips64el, ppc64el, s390x], 1.3-8 b3 [riscv64])
archiving and postprocessing for reference-compressed genomic multi-alignments
hdf-compass (0.7~b15-1)
viewer for HDF5 and related formats
hdf5-filter-plugin (0.0~git20221111.49e3b65-4 b3 [arm64, riscv64], 0.0~git20221111.49e3b65-4 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
external filters for HDF5: LZ4, BZip2, Bitshuffle
hdf5-filter-plugin-blosc-serial (0.0~git20220616.9683f7d-5 b3 [arm64, riscv64], 0.0~git20220616.9683f7d-5 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
blocking, shuffling and lossless compression library
hdf5-filter-plugin-zfp-serial (1.1.1-2 b3 [arm64], 1.1.1-2 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64])
Compression plugin for the HDF5 library using ZFP compression
hdf5-helpers (1.14.5 repack-1)
HDF5 - Helper tools
hdf5-tools (1.14.5 repack-1)
HDF5 - Runtime tools
herisvm (0.9.0-2)
machine learning tools for classification algorithms
heudiconv (1.3.2-1)
DICOM converter with support for structure heuristics
hfst-ospell (0.5.4-1 b2)
Spell checker library and tool based on HFST
hhsuite (3.3.0 ds-8 b3 [riscv64], 3.3.0 ds-8 b2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el])
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)
hinge (0.5.0-7 b3 [arm64], 0.5.0-7 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64])
long read genome assembler based on hinging
hisat2 (2.2.1-5 b2 [arm64], 2.2.1-5 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 2.2.1-5 [riscv64])
graph-based alignment of short nucleotide reads to many genomes
hmmer (3.4 dfsg-2 b1 [arm64], 3.4 dfsg-2 [amd64, i386])
profile hidden Markov models for protein sequence analysis
hmmer2 (2.3.2 dfsg-12 b1)
profile hidden Markov models for protein sequence analysis
hodie (1.5.0-4 b1 [arm64], 1.5.0-4 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
prints the date in Latin
horae (071~svn537 ds1-1) [contrib]
interactive graphical processing and analysis of EXAFS data
hpcc (1.5.0-4 b1)
HPC Challenge benchmark
htcondor (23.6.2 dfsg-2)
transitional dummy package
htcondor-annex-ec2 (23.6.2 dfsg-2)
transitional dummy package
htcondor-test (23.6.2 dfsg-2)
transitional dummy package
htcondor-upgrade-checks (23.6.2 dfsg-2)
transitional dummy package
hyphy-common (2.5.63 dfsg-1)
Hypothesis testing using Phylogenies (common files)
hyphy-mpi (2.5.63 dfsg-1 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 2.5.63 dfsg-1 [armel, armhf, i386])
Hypothesis testing using Phylogenies (MPI version)
hyphy-pt (2.5.63 dfsg-1 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 2.5.63 dfsg-1 [armel, armhf, i386])
Hypothesis testing using Phylogenies (pthreads version)
idba (1.1.3-8 b1 [arm64, riscv64], 1.1.3-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
iterative De Bruijn Graph short read assemblers
idba-extra (1.1.3-8 b1 [arm64, riscv64], 1.1.3-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
iterative De Bruijn Graph short read assemblers (extra tools)
ifeffit (2:1.2.11d-12.6 b1)
Interactive XAFS analysis program
igblast (1.19.0-1 b2 [arm64, riscv64], 1.19.0-1 b1 [amd64, mips64el, ppc64el, s390x])
Immunoglobulin and T cell receptor variable domain sequence analysis
igor (1.4.0 dfsg-5 b1)
infers V(D)J recombination processes from sequencing data
igv (2.18.5 dfsg-1)
Integrative Genomics Viewer
illustrate (0.0 git20200923.217db48-2 b2 [arm64], 0.0 git20200923.217db48-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
cartoonish representations of large biological molecules
imagej (1.54g-1)
Image processing program with a focus on microscopy images
imview (1.1.9h-4 b3 [arm64], 1.1.9h-4 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Image viewing and analysis application
indelible (1.03-6 b1 [arm64], 1.03-6 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
powerful and flexible simulator of biological evolution
indi-aagcloudwatcher-ng (1.7 20230106180155-1 b1 [arm64, riscv64], 1.7 20230106180155-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for the AAG Cloud Watcher
indi-aok (2.0 20221222093242-1 b2 [arm64, riscv64], 2.0 20221222093242-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for AOK Skywalker
indi-apogee (1.9 20221223184417-2 b1 [arm64], 1.9 20221223184417-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Apogee CCDs and Filter Wheels
indi-armadillo-platypus (1.0 20221226082641-2 b2 [arm64], 1.0 20221226082641-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Lunatico Astronomia Armadillo and Platypus
indi-asi (2.2 20221225102500-1) [contrib]
INDI Driver for ZWO Optics ASI cameras
indi-astrolink4 (0.1 20221223182627-1 b1 [arm64, riscv64], 0.1 20221223182627-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Astrolink 4.0 devices
indi-astromechfoc (0.2 20221223181816-1 b1 [arm64, riscv64], 0.2 20221223181816-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Astromechanics Canon Lens Controller
indi-avalon (1.12 20221223132122-1 b1 [arm64, riscv64], 1.12 20221223132122-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Avalon Instruments mounts
indi-beefocus (0.1 20221222010828-1 b1 [arm64, riscv64], 0.1 20221222010828-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Bee Focus
indi-bresserexos2 (1.0 20221223130124-1 b2 [arm64, riscv64], 1.0 20221223130124-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Exos II GoTo Telescope Mount
indi-dreamfocuser (2.1 20221223125100-1 b1 [arm64, riscv64], 2.1 20221223125100-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for DeamFocuser focuser
indi-dsi (0.4 20221223123028-2 b1 [arm64], 0.4 20221223123028-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Meade DSI Pro I/II/III
indi-eqmod (1.0 20230126190232-1 b2 [arm64, riscv64], 1.0 20230126190232-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI EQMod Driver
indi-ffmv (0.3 20221223120905-2 b2 [arm64], 0.3 20221223120905-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Point Grey Firefly MV cameras
indi-fishcamp (1.1-2) [contrib]
INDI driver for Fishcamp Engineering CCD
indi-fli (1.5 20221225141318-1 b1 [arm64, riscv64], 1.5 20221225141318-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for FLI CCD & Focuser
indi-gige (0.1 20221223115700-2 b1 [arm64], 0.1 20221223115700-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for GigE machine vision cameras
indi-gphoto (3.2 20221221172841-2 b3 [arm64], 3.2 20221221172841-2 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for GPhoto (DSLR) Cameras
indi-gpsd (0.5 20221222000619-1 b4 [arm64], 0.5 20221222000619-1 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for gpsd GPS daemon
indi-gpsnmea (0.2 20221223114018-1 b1 [arm64, riscv64], 0.2 20221223114018-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for GPS NMEA streams
indi-inovaplx (1.4 20221221105828-2) [contrib]
INDI driver for iNova PLX Cameras
indi-limesdr (1.4 20221223110308-1 b2 [arm64, riscv64], 1.4 20221223110308-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for LimeSDR (LMS7) Receiver
indi-maxdomeii (1.3 20221223105522-1 b1 [arm64, riscv64], 1.3 20221223105522-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for MaxDome II dome control system
indi-mgen (0.1 20221222184336-1 b1 [arm64, riscv64], 0.1 20221222184336-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Lacerta MGen Autoguider
indi-mi (1.8-1) [contrib]
INDI driver for cameras made by Moravian Instruments
indi-nexdome (1.5 20221222183051-1 b1 [arm64, riscv64], 1.5 20221222183051-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for NexDome
indi-nightscape (1.0.6 20221222181314-2 b2 [arm64], 1.0.6 20221222181314-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Celestron Nightscape 8300
indi-orion-ssg3 (0.1 20221222180647-2 b2 [arm64], 0.1 20221222180647-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI Driver for Orion StarShoot G3 and G4 cameras
indi-pentax (1.0 20221221102411-2) [contrib]
INDI driver for Pentax cameras
indi-playerone (0.9 20230105184731-3) [contrib]
INDI driver for cameras made by Playerone
indi-rtklib (1.0 20221222172722-1 b1 [arm64, riscv64], 1.0 20221222172722-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for precise positioning with RTKLIB
indi-sbig (2.1 20221220234924-4) [contrib]
INDI driver for SBIG cameras
indi-shelyak (1.0 20221222171819-1 b1 [arm64, riscv64], 1.0 20221222171819-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Shelyak and Alpy Spectrograph
indi-spectracyber (1.3 20221222164952-1 b2 [arm64, riscv64], 1.3 20221222164952-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for hydrogen line spectrometer
indi-starbook (0.8 20221222163625-1 b2 [arm64, riscv64], 0.8 20221222163625-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Vixen Starbook telescope controllers
indi-starbook-ten (0.1-2 b3 [arm64], 0.1-2 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Vixen Starbook Ten telescope controllers
indi-sx (1.16 20221222162728-2 b2 [arm64], 1.16 20221222162728-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
INDI driver for Starlight Xpress CCD and Filter Wheel
indi-talon6 (2.0 20221222160901-1 b1 [arm64, riscv64], 2.0 20221222160901-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for Talon6 Roll Off Roof
indi-webcam (1.0 20221222161740-1 b2)
INDI Driver for web cameras
indi-weewx-json (1.0-1 b2 [amd64, arm64, riscv64], 1.0-1 b1 [armel, armhf, i386, mips64el, ppc64el, s390x])
INDI driver for the WeeWX Weather Station
indigo-utils (1.2.3-3.1 b1 [arm64, riscv64], 1.2.3-3.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Organic Chemistry Toolkit Utilities
infernal (1.1.5-3)
inference of RNA secondary structural alignments
inhomog (0.1.9.2-1 b4 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.1.9.2-1 b2 [riscv64])
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 (2.0.1-1)
sequencing simulator producing realistic Illumina reads
ipig (0.0.r5-5)
integrating PSMs into genome browser visualisations
iqtree (2.0.7 dfsg-1 b2)
efficient phylogenetic software by maximum likelihood
iraf (2.18.1~rc1-2)
Image Reduction and Analysis Facility
iraf-dev (2.18.1~rc1-2)
Image Reduction and Analysis Facility (development files)
iraf-fitsutil (2024.07.06-1)
FITS utilities for IRAF
iraf-mscred (5.05 2018.07.09-3 b1)
CCD mosaic reduction package for IRAF
iraf-noao (2.18.1~rc1-2)
IRAF NOAO data reduction package
iraf-noao-dev (2.18.1~rc1-2)
IRAF NOAO data reduction package (development files)
iraf-rvsao (2.8.5-2 b1)
IRAF package to obtain radial velocities from spectra
iraf-sptable (1.0~pre20180612-3 b1)
IRAF package for Tabular Spectra
iraf-st4gem (1.0 ds-3)
Selected tools from the Space Telescope Science Data Analysis System
iraf-wcstools (3.9.7-1.1)
Handle the WCS of a FITS image (IRAF package)
iraf-xdimsum (2003.01.24-2)
Deep Infrared Mosaicing Software
irstlm (6.00.05-5)
IRST Language Modeling Toolkit
ismrmrd-schema (1.8.0-2)
schema for ISMRMRD
ismrmrd-tools (1.8.0-2 b6)
command-line tools for ISMRMRD
iso2mesh-demos (1.9.8 ds-1)
sample files and demo scripts for Iso2Mesh toolbox
iso2mesh-tools (1.9.8 ds-1)
3D mesh generation and repairing utilities
iva (1.0.11 ds-6)
iterative virus sequence assembler
ivar (1.4.3 dfsg-2 b1 [arm64], 1.4.3 dfsg-2 [amd64, i386, mips64el, riscv64])
functions broadly useful for viral amplicon-based sequencing
jaligner (1.0 dfsg-11)
Smith-Waterman algorithm with Gotoh's improvement
jalview (2.11.4.0 dfsg-3)
multiple alignment editor
jblas (1.2.5 dfsg-1 b1 [riscv64], 1.2.5 dfsg-1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
fast linear algebra library for Java
jbmc (6.1.1-2)
bounded model checker for Java programs
jellyfish (2.3.1-4)
count k-mers in DNA sequences
jellyfish-examples (2.3.1-4)
count k-mers in DNA sequences (examples for testing)
jellyfish1 (1.1.11-9 b1 [arm64, riscv64], 1.1.11-9 [amd64, mips64el, ppc64el])
count k-mers in DNA sequences
jemboss (6.6.0 dfsg-15)
graphical user interface to EMBOSS
jmodeltest (2.1.10 dfsg-12)
HPC selection of models of nucleotide substitution
jmol (16.2.33 dfsg-1)
Molecular Viewer
jnifti-demos (0.6-3)
sample files and demo scripts for JNIfTI toolbox
jsamp (1.3.9-1)
Java Simple Application Messaging Protocol tool for VO
jube (2.7.1-2)
JUBE Benchmarking Environment
jupyter-notebook (6.4.13-5)
Jupyter interactive notebook
kalign (1:3.4.0-1 b2)
Global and progressive multiple sequence alignment
kallisto (0.48.0 dfsg-4 b3 [mips64el], 0.48.0 dfsg-4 b2 [arm64, riscv64], 0.48.0 dfsg-4 b1 [amd64, ppc64el, s390x])
near-optimal RNA-Seq quantification
kallisto-examples (0.48.0 dfsg-4)
near-optimal RNA-Seq quantification (example data)
kalzium (4:23.08.5-1 b1 [arm64], 4:23.08.5-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
periodic table and chemistry tools
kalzium-data (4:23.08.5-1)
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
kineticstools (0.6.1 git20220223.1326a4d dfsg-3)
detection of DNA modifications
kineticstools-data (0.6.1 git20220223.1326a4d dfsg-3)
detection of DNA modifications -- data files
king-probe (02.21-1 b1 [arm64, riscv64], 02.21-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Evaluate and visualize protein interatomic packing
kissat (4.0.1-3)
Keep it simple and clean bare metal SAT solver
kissplice (2.6.7-1)
Detection of various kinds of polymorphisms in RNA-seq data
kleborate (2.4.1-3)
tool to screen Klebsiella genome assemblies
kleborate-examples (2.4.1-3)
tool to screen Klebsiella genome assemblies (example data)
klustakwik (3.0.2 ds-2 b1 [arm64, riscv64], 3.0.2 ds-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
automatic sorting of the samples (spikes) into clusters
kma (1.4.15-1)
mapping genomic sequences to raw reads directly against redundant databases
kmc (3.2.4 dfsg-1 b2)
count kmers in genomic sequences
kmer (0~20150903 r2013-9)
suite of tools for DNA sequence analysis
kmer-examples (0~20150903 r2013-9)
sample data for kmer suite of tools for DNA sequence analysis
kmerresistance (2.2.0-4 b1 [arm64, riscv64], 2.2.0-4 [amd64, mips64el, ppc64el, s390x])
correlates mapped genes with the predicted species of WGS samples
konclude (0.7.0 1138 git20220514~dfsg-1 b2 [arm64, riscv64], 0.7.0 1138 git20220514~dfsg-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
tableau-based description logic reasoner for the semantic web
kraken (1.1.1-4 b1 [arm64, riscv64], 1.1.1-4 [amd64, mips64el, ppc64el])
assigning taxonomic labels to short DNA sequences
kraken2 (2.1.3-1 b1 [arm64, riscv64], 2.1.3-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
taxonomic classification system using exact k-mer matches
kst (2.0.8-6 b2)
scientific data plotting tool
kstars (5:3.6.2-2 b7 [armel, armhf], 5:3.6.2-2 b5 [amd64, arm64, i386, mips64el, ppc64el, s390x], 5:3.6.2-2 b4 [riscv64])
desktop planetarium, observation planning and telescope control
kstars-data (5:3.6.2-2)
data files for KStars desktop planetarium
kstars-data-extra-tycho2 (1.1r1-9.1) [non-free]
Tycho-2 star catalog for KStars
lagan (2.0-10 b1 [arm64], 2.0-10 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
highly parametrizable pairwise global genome sequence aligner
lamarc (2.1.10.1 dfsg-7 b5 [arm64, mips64el], 2.1.10.1 dfsg-7 b4 [amd64, armel, armhf, i386, ppc64el, s390x], 2.1.10.1 dfsg-7 b3 [riscv64])
Likelihood Analysis with Metropolis Algorithm using Random Coalescence
lamassemble (1.7.2-2)
Merges overlapping "long" DNA reads into a consensus sequences
lambda-align (1.0.3-6 b1 [arm64, riscv64], 1.0.3-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Local Aligner for Massive Biological DatA
lambda-align2 (2.0.1-3)
Local Aligner for Massive Biological DatA - v2
lammps (20240207 dfsg-2)
Molecular Dynamics Simulator
last-align (1542-1 b2)
genome-scale comparison of biological sequences
lastz (1.04.22-2 b1 [arm64, riscv64], 1.04.22-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
pairwise aligning DNA sequences
lastz-examples (1.04.22-2)
pairwise aligning DNA sequences (examples and test scripts)
lbt (1.2.2-7 b1 [arm64, riscv64], 1.2.2-7 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
converts from LTL formulas to Büchi automata
leaff (0~20150903 r2013-9)
biological sequence library utilities and applications
lefse (1.1.2-2)
determine features of organisms, clades, taxonomic units, genes
libatlas-ecmwf-utils (0.40.0-1)
Numerical weather prediction and climate modelling library - utilities
libbio-db-hts-perl (3.01-5)
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 (1.7.4-4)
Bioperl interface to Clustal W
libca4.14.4 (7.0.8.1 dfsg1-6)
EPICS channel access client library
libcg3-1 (1.4.6-1 b3)
Runtime for CG-3
libchemicaltagger-java (1.6.2-4)
tool for semantic text-mining in chemistry
libcom3.23.1 (7.0.8.1 dfsg1-6)
EPICS common library
libdbcsr-dev (2.6.0-2)
Distributed Block Compressed Sparse Row matrix library
libdlpack-dev (1.0-1)
Open In Memory Tensor Structure
libeccodes-data (2.39.1-1)
GRIB and BUFR enecoding/encoding software library - data
libeckit-utils (1.28.3-1 b1)
C toolkit for ECMWF tools and applications - development files
libfaiss-dev (1.9.0-5 b1)
efficient similarity search and clustering of dense vectors
libfckit-utils (0.13.2-1)
Library Fortran toolkit for interoperating Fortran with C/C
libgoby-io-java (3.3.1 dfsg2-11)
IO API for goby
libhdf5-jni (1.14.5 repack-1)
native library used by libhdf5-java
libideep-dev (0.0~git20240814.41d636c-1)
Intel's mkldnn/dnnl wrapper for pytorch
libinchi-bin (1.07.1 dfsg-6)
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-2)
Molecular Dynamics Simulator (dev files)
liblammps0t64 (20240207 dfsg-2)
Molecular Dynamics Simulator (shared library)
liblemon-utils (1.3.1 dfsg-6 b2)
Library for Efficient Modeling and Optimization in Networks (utilities)
liblinear-tools (2.3.0 dfsg-5 b2)
Standalone applications for LIBLINEAR
libmcpl-dev (1.3.2-3.1 b1 [arm64, riscv64], 1.3.2-3.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Monte Carlo Particle Lists - development files
libmcpl1 (1.3.2-3.1 b1 [arm64, riscv64], 1.3.2-3.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Monte Carlo Particle Lists - library
libmstoolkit-tools (82-7.2)
libraries for manipulating mass spectrometry data - tools
libocas-tools (0.97 dfsg-8 b2)
Standalone applications implementing the OCAS solver
libonnx-dev (1.16.2-1 b1)
Open Neural Network Exchange (ONNX) (dev)
libonnx-testdata (1.16.2-1)
Open Neural Network Exchange (ONNX) (test data)
libonnx1t64 (1.16.2-1 b1)
Open Neural Network Exchange (ONNX) (libs)
libopm-simulators-bin (2024.10 ds-3 b2)
Parallel porous media / reservoir simulators -- applications
libopm-upscaling-bin (2024.10 ds-1 b1)
Porous media upscaling tools -- applications
liboscar4-java (5.2.0 dfsg-2)
automated annotation of chemistry in scientific articles
libphitsmcpl1 (1.3.2-3.1 b1 [arm64, riscv64], 1.3.2-3.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Monte Carlo Particle Lists - PHITS library
libpluto-jpl-eph-dev (0.0~git20180228-1.1 b1 [arm64, riscv64], 0.0~git20180228-1.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
development files to interact with JPL ephemeres data
libpluto-lunar-dev (0.0~git20180825.e34c1d1-1 b1 [amd64, arm64, riscv64], 0.0~git20180825.e34c1d1-1 [armel, armhf, i386, mips64el, ppc64el, s390x])
development files for astronomical Lunar library
libqgis-customwidgets (3.34.13 dfsg-1)
QGIS custom widgets for Qt Designer
libsigmf (1.0.2-3)
SigMF data format handling library
libsilo-bin (4.11-6.1 b2)
Utilities to manipulate libsilo files
libsmiles-scripts-java (0.2.0 dfsg1-6)
command line tools to handle SMILES descriptors - Java libraries
libsmiles-scripts-perl (0.2.0 dfsg1-6)
command line tools to handle SMILES descriptors - Perl libraries
libssm-bin (1.4.0-2 b3)
macromolecular superposition library - binaries
libsswmcpl1 (1.3.2-3.1 b1 [arm64, riscv64], 1.3.2-3.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Monte Carlo Particle Lists - SSW library
libtrexio0 (2.2.3-3 b3)
TREX I/O library for efficient data I/O in quantum chemistry.
libuhd4.7.0-dpdk-tests (4.7.0.0 ds1-2 b2)
universal hardware driver for Ettus Research products - DPDK tests
libvcflib-tools (1.0.9 dfsg1-3 b2)
C library for parsing and manipulating VCF files (tools)
libvdjtools-java (1.2.1 git20190311 repack-2) [non-free]
Java library of vdjtools
libwannier90-dev (3.1.0 ds-10)
Maximally Localized Wannier Functions - development library
libxgboost-dev (2.1.3-1)
Scalable and Flexible Gradient Boosting (Development)
libxgboost-predictor-java (0.3.1 dfsg-2)
Java implementation of XGBoost predictor for online prediction tasks
libxgboost0 (2.1.3-1)
Scalable and Flexible Gradient Boosting (Shared lib)
libxy-bin (1.6-3.1 b4)
xylib - utilities
libyade (2024.08a-4 b1)
Platform for discrete element modeling. Libraries
liggghts (3.8.0 repack1-12)
Open Source DEM Particle Simulation Software.
lighter (1.1.3-1)
fast and memory-efficient sequencing error corrector
litl-tools (0.1.9-13 b2)
Lightweight Trace Library - tools
llm (0.19.1-1) [contrib]
CLI utility and Python library for interacting with Large Language Models
loki (2.4.7.4-12)
MCMC linkage analysis on general pedigrees
looktxt (1.4.1-3 b1 [arm64, riscv64], 1.4.1-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Convert free format text file into scientific data formats
looptools (2.16-1 b1 [riscv64], 2.16-1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Integral Evaluator of One-loop Feynman Diagram
lorene (0.0.0~cvs20161116 dfsg-1.3)
framework for numerical relativity
lorene-codes-src (0.0.0~cvs20161116 dfsg-1.3)
source files of LORENE-based codes
ltrsift (1.0.2-10 b1 [arm64], 1.0.2-10 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
postprocessing and classification of LTR retrotransposons
lttoolbox-dev (3.7.6-1 b2)
Development tools and library for lttoolbox
lucy (1.20-5 b1 [arm64], 1.20-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
DNA sequence quality and vector trimming tool
lumpy-sv (0.3.1 dfsg-7 b2 [riscv64], 0.3.1 dfsg-7 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el])
general probabilistic framework for structural variant discovery
lumpy-sv-examples (0.3.1 dfsg-7)
general probabilistic framework for structural variant discovery (data)
lutefisk (1.0.7 dfsg-7 b1 [arm64, riscv64], 1.0.7 dfsg-7 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
de novo interpretation of peptide CID spectra
lxi-tools (2.7-1 b2 [arm64, riscv64], 2.7-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
LAN eXtensions for Instrumentation (LXI) software interface
m2kcli (0.9.0-3)
ADI tool for interfacing with the ADALM2000
macs (3.0.2-1 b1)
Model-based Analysis of ChIP-Seq on short reads sequencers
macsyfinder (2.1.4-1)
detection of macromolecular systems in protein datasets
maffilter (1.3.1 dfsg-6 b1 [arm64], 1.3.1 dfsg-6 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
process genome alignment in the Multiple Alignment Format
maffilter-examples (1.3.1 dfsg-6)
process genome alignment in the Multiple Alignment Format (example data)
mafft (7.505-1 b1 [arm64, riscv64], 7.505-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (3.2.1-10.1 b2)
Solver for Mandelbrot polynomials based on MPSolve
mapdamage (2.2.2 dfsg-1)
tracking and quantifying damage patterns in ancient DNA sequences
mapsembler2 (2.2.4 dfsg1-4 b1 [arm64], 2.2.4 dfsg1-4 [amd64, ppc64el, s390x])
bioinformatics targeted assembly software
maq (0.7.1-10)
maps short fixed-length polymorphic DNA sequence reads to reference sequences
maqview (0.2.5-12)
graphical read alignment viewer for short gene sequences
mash (2.3 dfsg-6 b2 [riscv64], 2.3 dfsg-6 b1 [amd64, arm64, mips64el, ppc64el, s390x])
fast genome and metagenome distance estimation using MinHash
matlab-brain2mesh (0.7.9-3) [contrib]
automated brain tetrahedral mesh generation toolbox for MATLAB
matlab-gdf (0.1.3-11.1) [contrib]
IO library for the GDF -- Matlab interface
matlab-iso2mesh (1.9.8 ds-1) [contrib]
3D surface and volumetric mesh generator for MATLAB
matlab-jnifti (0.6-3) [contrib]
fast NIfTI-1/2 reader and NIfTI-to-JNIfTI converter for MATLAB
matlab-jsonlab (2.9.8-1) [contrib]
native JSON/UBJSON/MassagePack encoder/decoder for MATLAB
matlab-zmat (0.9.9 ds.1-3) [contrib]
in-memory data compression for MATLAB
maude (3.4-1 b1 [arm64], 3.4-1 [amd64, mips64el, ppc64el, riscv64, s390x])
high-performance logical framework
mauve-aligner (2.4.0 4736-6)
multiple genome alignment
mayavi2 (4.8.2-4)
scientific visualization package for 2-D and 3-D data
mbpoll (1.5.2-1)
command line utility to communicate with ModBus slave (RTU or TCP)
mbt (3.10-3 b1)
memory-based tagger-generator and tagger
mbtserver (0.16-2 b1 [arm64], 0.16-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Server extensions for the MBT tagger
mcaller (1.0.3 git20210624.b415090-3)
find methylation in nanopore reads
mcpl (1.3.2-3.1 b1 [arm64, riscv64], 1.3.2-3.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Monte Carlo Particle Lists - libraries and tools
mcstas (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation
mcstas-clusterscripts (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - parallelization scripts
mcstas-comps (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - components
mcstas-manuals (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - documentation
mcstas-mccodelib (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - Python code library
mcstas-mcdisplay-mantid (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - Mantid instrument display
mcstas-mcdisplay-matlab (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - Matlab/Octave instrument display
mcstas-mcdisplay-matplotlib (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - Matplotlib instrument display
mcstas-mcdisplay-pyqtgraph (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - pyqtgraph instrument display
mcstas-mcdisplay-webgl (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - WebGL instrument display
mcstas-mcdisplay-webgl-classic (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - WebGL instrument display
mcstas-mcdoc (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - documentation browser
mcstas-mcgui (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - GUI
mcstas-mcplot-matlab (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - Matlab/Octave plotting frontend
mcstas-mcplot-matplotlib (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - Matplotlib plotting frontend
mcstas-mcplot-pyqtgraph (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - pyqtgraph plotting frontend
mcstas-mcplot-svg (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - SVG plotting frontend
mcstas-mcresplot (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - resolution function plotter
mcstas-mcrun (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - runner
mcstas-suite-python (3.5 0.0~git20240801183257.cdaa431 ds5-2)
Neutron ray-trace simulation - full simulation suite
mcxtrace (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation
mcxtrace-clusterscripts (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - parallelization scripts
mcxtrace-comps (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - components
mcxtrace-manuals (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - documentation
mcxtrace-mccodelib (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - Python code library
mcxtrace-mxdisplay-matlab (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - Matlab/Octave instrument display
mcxtrace-mxdisplay-matplotlib (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - Matplotlib instrument display
mcxtrace-mxdisplay-pyqtgraph (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - pyqtgraph instrument display
mcxtrace-mxdisplay-webgl (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - WebGL instrument display
mcxtrace-mxdisplay-webgl-classic (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - WebGL instrument display
mcxtrace-mxdoc (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - documentation browser
mcxtrace-mxgui (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - GUI
mcxtrace-mxplot-matlab (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - Matlab/Octave plotting frontend
mcxtrace-mxplot-matplotlib (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - Matplotlib plotting frontend
mcxtrace-mxplot-pyqtgraph (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - pyqtgraph plotting frontend
mcxtrace-mxplot-svg (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - SVG plotting frontend
mcxtrace-mxrun (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - runner
mcxtrace-suite-python (3.5 0.0~git20240801183257.cdaa431 ds5-2)
X-ray ray-trace simulation - full simulation suite
mecat2 (0.0 git20200428.f54c542 ds-4)
ultra-fast and accurate de novo assembly tools for SMRT reads
meep (1.25.0-4 b1)
software package for FDTD simulation
megadepth (1.2.0-4 b2 [arm64, riscv64], 1.2.0-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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-4)
interactive tool to explore and analyse microbiome sequencing data
melting (5.2.0-2)
compute the melting temperature of nucleic acid duplex
merkaartor (0.20.0 ds-1)
map editor for OpenStreetMap.org
meryl (0~20150903 r2013-9)
in- and out-of-core kmer counting and utilities
metabat (2.15-4 b1)
robust statistical framework for reconstructing genomes from metagenomic data
metaeuk (7-bba0d80 ds-1 b1)
sensitive, high-throughput gene discovery and annotation for metagenomics
metaeuk-examples (7-bba0d80 ds-1)
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 (2.0.1-10)
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 (5.23.1-1)
Interactive data visualization and analysis environment,
metview-data (5.23.1-1)
Data needed for the Metview data analysis environment
mhap (2.1.3 dfsg-3)
locality-sensitive hashing to detect long-read overlaps
microbegps (1.0.0-7)
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 (5.3.3 repack-1)
hardware & software framework to learn microcontrollers
minc-tools (2.3.00 dfsg-10 b2 [arm64, riscv64], 2.3.00 dfsg-10 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
MNI medical image format tools
minexpert2 (9.6.0-1)
MS^n mass spectrometric data visualization and mining (runtime)
minia (3.2.6-4 b3 [arm64], 3.2.6-4 b2 [amd64, mips64el, ppc64el, riscv64])
short-read biological sequence assembler
miniasm (0.3 dfsg-4 b1 [arm64, riscv64], 0.3 dfsg-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
ultrafast de novo assembler for long noisy DNA sequencing reads
minicondor (23.6.2 dfsg-2)
distributed workload management system - single node configuration
minihtcondor (23.6.2 dfsg-2)
transitional dummy package
minimac4 (4.1.6-1)
Fast Imputation Based on State Space Reduction HMM
minimap (0.2-8 b2)
tool for approximate mapping of long biosequences such as DNA reads
minimap2 (2.27 dfsg-1 b3 [arm64], 2.27 dfsg-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
versatile pairwise aligner for genomic and spliced nucleotide sequences
minisat (1:2.2.1-8 b1 [arm64], 1:2.2.1-8 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Fast and lightweight SAT solver
minisat (1.0-5)
solver for pseudo-Boolean constraints
mipe (1.1-9)
Tools to store PCR-derived data
mira-assembler (4.9.6-11 b1 [arm64], 4.9.6-11 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Whole Genome Shotgun and EST Sequence Assembler
mira-rfam-12s-rrna (4.9.6-11)
extract of RFAM 12 rRNA database
mirtop (0.4.28-2)
annotate miRNAs with a standard mirna/isomir naming
missfits (2.8.0-5 b1 [arm64, riscv64], 2.8.0-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Basic maintenance and packaging tasks on FITS files
mitools (2.0.5-7)
view, convert and perform basic maths with medical image datasets
mlpack-bin (4.5.1-1)
intuitive, fast, scalable C machine learning library (binaries)
mmb (4.0.0 dfsg-5)
model the structure and dynamics of macromolecules
mmb-common (4.0.0 dfsg-5)
model the structure and dynamics of macromolecules (common files)
mmmulti (0.1-3)
memory backed multimap
mmseqs2 (15-6f452 ds-2 b3 [riscv64], 15-6f452 ds-2 b2 [amd64, arm64, mips64el, ppc64el])
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 b1 [arm64, riscv64], 2.02.73.2-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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
molds (0.3.1-2 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 0.3.1-2 [armhf, i386])
Semi-empirical electronic structure and molecular dynamics
molequeue (0.9.0-1 b3 [amd64], 0.9.0-1 b2 [arm64, riscv64], 0.9.0-1 b1 [armel, armhf, i386, mips64el, ppc64el, s390x])
Desktop integration of high performance computing resources
mona (1.4-18-1 b2 [arm64], 1.4-18-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
theorem prover based on automata
montage (6.0 dfsg-10 b1)
Toolkit for assembling FITS images into mosaics
montage-gridtools (6.0 dfsg-10 b1)
Create files to run montage on the grid
mopac (22.1.1-2 b1 [arm64], 22.1.1-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Molecular Orbital PACkage (MOPAC)
mopac7-bin (1.15-7)
Semi-empirical Quantum Chemistry Library (binaries)
mothur (1.48.1-1 b1 [arm64], 1.48.1-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
sequence analysis suite for research on microbiota
mpb (1.11.1-6 b2 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 1.11.1-6 b1 [armel, armhf, i386])
MIT Photonic-Bands
mpb-mpi (1.11.1-6 b2 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 1.11.1-6 b1 [armel, armhf, i386])
MIT Photonic-Bands, parallel (mpich) version
mpb-scm (1.11.1-6)
MIT Photonic-Bands initialisation files
mpgrafic (0.3.19-1 b6 [s390x], 0.3.19-1 b5 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el], 0.3.19-1 b4 [riscv64])
MPI version of N-body initial conditions grafic package
mpsolve (3.2.1-10.1 b2)
Multiprecision polynomial solver (command line version)
mptp (0.2.5-1)
single-locus species delimitation
mrbayes (3.2.7a-7 b2 [arm64], 3.2.7a-7 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Bayesian Inference of Phylogeny
mrbayes-mpi (3.2.7a-7 b2 [arm64], 3.2.7a-7 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Bayesian Inference of Phylogeny - mpi version
mricron (1.2.20211006 dfsg-6)
magnetic resonance image conversion, viewing and analysis
mricron-data (1.2.20211006 dfsg-6)
data files for MRIcron
mrpt-apps (1:2.14.7 ds-1)
Mobile Robot Programming Toolkit - Console and GUI applications
mrpt-common (1:2.14.7 ds-1)
Mobile Robot Programming Toolkit - Example datasets and files
mrtrix3 (3.0.4-1 b2 [arm64], 3.0.4-1 b1 [amd64])
diffusion-weighted MRI white matter tractography
mseed2sac (2.3 ds1-1 b1 [arm64, riscv64], 2.3 ds1-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Convert MiniSEED time series data to SAC
mssstest (3.0-7) [non-free]
Normalisation of disease scores for patients with Multiple Sclerosis
multiqc (1.21 dfsg-2)
output integration for RNA sequencing across tools and samples
mumax3 (3.10-9) [contrib]
GPU-accelerated micromagnetic simulator
mummer (3.23 dfsg-8 b1 [arm64, riscv64], 3.23 dfsg-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Efficient sequence alignment of full genomes
munipack (0.6.1-1)
Astronomical photometry software package
munipack-cli (0.6.1-1 b8 [armhf], 0.6.1-1 b7 [arm64, armel, mips64el], 0.6.1-1 b6 [amd64, i386, ppc64el, s390x], 0.6.1-1 b4 [riscv64])
Command line interface of Munipack
munipack-core (0.6.1-1 b8 [armhf], 0.6.1-1 b7 [arm64, armel, mips64el], 0.6.1-1 b6 [amd64, i386, ppc64el, s390x], 0.6.1-1 b4 [riscv64])
Core routines of Munipack
munipack-gui (0.6.1-1 b8 [armhf], 0.6.1-1 b7 [arm64, armel, mips64el], 0.6.1-1 b6 [amd64, i386, ppc64el, s390x], 0.6.1-1 b4 [riscv64])
Graphical user interface of Munipack
murasaki (1.68.6-14 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 1.68.6-14 [armel, armhf, i386])
homology detection tool across multiple large genomes
murasaki-common (1.68.6-14)
homology detection tool across multiple large genomes (common files)
murasaki-mpi (1.68.6-14 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 1.68.6-14 [armel, armhf, i386])
homology detection tool across multiple large genomes (MPI-version)
muscle (1:5.1.0-1 b1 [arm64, riscv64], 1:5.1.0-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Multiple alignment program of protein sequences
muscle3 (3.8.1551-3 b1 [arm64], 3.8.1551-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
multiple alignment program of protein sequences
mustang (3.2.4-1 b1 [arm64, riscv64], 3.2.4-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
multiple structural alignment of proteins
mustang-testdata (3.2.4-1)
multiple structural alignment of proteins, test data
nanolyse (1.2.0-4 b1 [riscv64], 1.2.0-4 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
remove lambda phage reads from a fastq file
nanook (1.33 dfsg-6)
pre- and post-alignment analysis of nanopore sequencing data
nanook-examples (1.33 dfsg-6)
pre- and post-alignment analysis of nanopore sequencing data (examples)
nanopolish (0.14.0-1 b3 [arm64, riscv64], 0.14.0-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el])
consensus caller for nanopore sequencing data
nanosv (1.2.4 git20190409.c1ae30c-7)
structural variant caller for nanopore data
nast-ier (20101212 dfsg1-6 b1 [arm64], 20101212 dfsg1-6 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
NAST-based DNA alignment tool
nautic (1.5-6 b5 [arm64, mips64el], 1.5-6 b4 [amd64, armel, armhf, i386, ppc64el, s390x], 1.5-6 b3 [riscv64])
computation of observer position in astro-navigation
ncbi-acc-download (0.2.8-3)
download genome files from NCBI by accession
ncbi-blast (2.16.0 ds-6 b1)
next generation suite of BLAST sequence search tools
ncbi-blast -legacy (2.16.0 ds-6)
NCBI Blast legacy call script
ncbi-cn3d (3.0.20170106 dfsg2-5)
3-dimensional viewer for biological molecules
ncbi-entrez-direct (19.2.20230331 dfsg-3 b4 [riscv64], 19.2.20230331 dfsg-3 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
NCBI Entrez utilities on the command line
ncbi-epcr (2.3.12-1-10 b1 [arm64], 2.3.12-1-10 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Tool to test a DNA sequence for the presence of sequence tagged sites
ncbi-rrna-data (6.1.20170106 dfsg2-5)
large rRNA BLAST databases distributed with the NCBI toolkit
ncbi-seg (0.0.20000620-7)
tool to mask segments of low compositional complexity in amino acid sequences
ncbi-tools-bin (6.1.20170106 dfsg2-5)
NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11 (6.1.20170106 dfsg2-5)
NCBI libraries for biology applications (X-based utilities)
ncl-tools (2.1.21 git20210811.b1213a7-6)
tools to deal with NEXUS files
nco (5.2.9-1)
Command-line operators to analyze netCDF files
ncoils (2002-9 b1 [arm64, riscv64], 2002-9 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
coiled coil secondary structure prediction
ncview (2.1.11 ds-1)
X11 visual browser for NetCDF format files
neat (2.3.2-2 b3 [amd64, arm64, armel, i386, mips64el, s390x], 2.3.2-2 b2 [armhf, ppc64el, riscv64])
Nebular Empirical Analysis Tool
neobio (0.0.20030929-6)
computes alignments of amino acid and nucleotide sequences
netcdf-bin (1:4.9.2-7 b1)
Programs for reading and writing NetCDF files
neurodebian (0.42.2)
neuroscience-oriented distribution - repository configuration
neurodebian-archive-keyring (0.42.2)
neuroscience-oriented distribution - GnuPG archive keys
neurodebian-desktop (0.42.2)
neuroscience-oriented distribution - desktop integration
neurodebian-dev (0.42.2)
neuroscience-oriented distribution - development tools
neurodebian-freeze (0.42.2)
nd_freeze tool to freeze APT sources to use snapshots
neurodebian-popularity-contest (0.42.2)
neuroscience-oriented distribution - popcon integration
neuron (8.2.2-7 b1 [amd64, arm64, ppc64el, riscv64, s390x], 8.2.2-7 [armel, armhf, i386])
Simulation environment for computational models of neurons
neuron-dev (8.2.2-7 b1 [amd64, arm64, ppc64el, riscv64, s390x], 8.2.2-7 [armel, armhf, i386])
Neuron simulation environment - Development files
nexus-tools (4.4.3-6 b3 [arm64, riscv64], 4.4.3-6 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
NeXus scientific data file format - applications
ngmlr (0.2.7 git20210816.a2a31fb dfsg-2 b2 [arm64], 0.2.7 git20210816.a2a31fb dfsg-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
CoNvex Gap-cost alignMents for Long Reads
njplot (2.4-9 b2 [arm64, riscv64], 2.4-9 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
phylogenetic tree drawing program
nmodl (0.6-2 b4 [arm64], 0.6-2 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 b1 [arm64, riscv64], 0.9 git220919-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
NMODL to C converter for CoreNEURON
ntcard (1.2.2 dfsg-9)
Streaming algorithm to estimate cardinality in genomics datasets
nthash (2.3.0 dfsg-2)
Methods to evaluate runtime and uniformity tests for hashing methods
numdiff (5.9.0-1 b1 [amd64, arm64, riscv64], 5.9.0-1 [armel, armhf, i386, mips64el, ppc64el, s390x])
Compare similar files with numeric fields
nutsqlite (2.0.6-4)
Dietary nutrition analysis software
nxtrim (0.4.3 dfsg-4)
Optimized trimming of Illumina mate pair reads
oar-common (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler common package
oar-node (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler node package
oar-server (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler server package
oar-server-mysql (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler MySQL server backend package
oar-server-pgsql (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler PostgreSQL server backend package
oar-user (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler user package
oar-user-mysql (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler MySQL user backend package
oar-user-pgsql (2.5.10-2 b1 [arm64], 2.5.10-2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
OAR batch scheduler PostgreSQL user backend package
oar-web-status (2.5.10-2)
OAR batch scheduler visualization tool package
objcryst-fox (2022.1-1 b6 [arm64], 2022.1-1 b5 [amd64, ppc64el, s390x], 2022.1-1 b3 [riscv64])
Free Objects for Xtallography
occt-draw (7.8.1 dfsg1-3)
Open CASCADE Technology command interpreter and graphical test system
octave-bart (0.9.00-3)
Octave bindings for BART
octave-biosig (2.6.1-1 b1)
Octave bindings for BioSig library
octave-brain2mesh (0.7.9-3)
automated brain tetrahedral mesh generation toolbox for Octave
octave-gdf (0.1.3-11.1 b1)
IO library for the GDF -- Octave interface
octave-iso2mesh (1.9.8 ds-1)
3D surface and volumetric mesh generator for Octave
octave-jnifti (0.6-3)
fast NIfTI-1/2 reader and NIfTI-to-JNIfTI converter
octave-jsonlab (2.9.8-1)
native JSON/UBJSON/MassagePack encoder/decoder for Octave
octave-psychtoolbox-3 (3.0.19.14.dfsg1-1)
toolbox for vision research -- Octave bindings
octave-zmat (0.9.9 ds.1-3)
in-memory data compression for Octave
octomap-tools (1.9.7 dfsg-4)
Tools for 3D occupancy grid mapping
octovis (1.9.7 dfsg-4)
Visualization tool for OctoMap
odil (0.12.2-5)
C 11 library for the DICOM standard (application)
odin (2.0.5-7)
develop, simulate and run magnetic resonance sequences
ogdi-bin (4.1.1 ds-5)
Open Geographic Datastore Interface Library -- utilities
ompl-plannerarena (1.6.0 ds1-1)
Open Motion Planning Library (OMPL) plannerarena
onnxruntime-tools (1.19.2 dfsg-2)
cross-platform inference and training ML accelerator (tools)
ont-fast5-api (4.1.1 dfsg-4 b1)
simple interface to HDF5 files of the Oxford Nanopore .fast5 file format
open3d-gui (0.18.0 ds-6)
Transitional dummy package for open3d-viewer
open3d-tools (0.18.0 ds-6)
Library for 3D data processing - tools
open3d-viewer (0.18.0 ds-6)
Library for 3D data processing - viewer GUI
open3d-viewer-data (0.18.0 ds-6)
Library for 3D data processing - viewer GUI resources
openbabel (3.1.1 dfsg-11 b1)
Chemical toolbox utilities (cli)
openbabel-gui (3.1.1 dfsg-11 b1)
Chemical toolbox utilities (graphical user interface)
opendrop (3.3.2-2 b2 [amd64, ppc64el, s390x], 3.3.2-2 b1 [arm64, armel, armhf, i386, mips64el, riscv64])
fully-featured pendant drop tensiometry software
openfoam (1912.200626-3 b1)
Open source toolbox for Computational Fluid Dynamics (CFD) - binaries
openfoam-examples (1912.200626-3)
Open source toolbox for Computational Fluid Dynamics (CFD) - examples
openmotor (0.5.0-3)
internal ballistics simulator for rocket motor experimenters
openms (2.6.0 cleaned1-4)
package for LC/MS data management and analysis
openms-common (2.6.0 cleaned1-4)
package for LC/MS data management and analysis - shared data
openstructure (2.9.0-2)
Open-Source Computational Structural Biology Framework
opentelemetry-proto (1.3.2-2)
OpenTelemetry protocol specification and proto files
openturns-common (1.23-5)
generic tool to treat and quantify uncertainties (common files)
openuniverse (1.0beta3.1 dfsg-7.1 b2 [arm64, riscv64], 1.0beta3.1 dfsg-7.1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
3D Universe Simulator
openuniverse-common (1.0beta3.1 dfsg-7.1)
3D Universe Simulator data files
optgeo (2.25-4)
simulator for geometrical optics
opticalraytracer (9.6-4)
Virtual lens/mirror design workshop
optimir (1.2-2)
Integrating genetic variations in miRNA alignment
orthanc (1.12.5 dfsg-1)
Lightweight, RESTful DICOM server for medical imaging
orthanc-dicomweb (1.18 dfsg-1)
Plugin to extend Orthanc with support of WADO and DICOMweb
orthanc-gdcm (1.8 dfsg-1 b1)
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-1 b5)
Plugins to use MySQL or MariaDB as a database back-end to Orthanc
orthanc-neuro (1.1 dfsg-1 b3)
Neuroimaging plugin for Orthanc
orthanc-postgresql (5.0 dfsg-3)
Plugins to use PostgreSQL as a database back-end to Orthanc
orthanc-python (4.3 ds-1 b2)
Develop plugins for Orthanc using the Python programming language
orthanc-webviewer (2.9 dfsg-1 b2)
Web viewer of medical images for Orthanc
orthanc-wsi (3.0 dfsg-1)
Whole-slide imaging support for Orthanc (digital pathology)
oscar (1.5.3-1 b1 [arm64], 1.5.3-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Open Source CPAP Analysis Reporter (OSCAR)
osra (2.1.3-3 b3 [riscv64], 2.1.3-3 b2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
optical structure recognition
otf-trace (1.12.5 dfsg-8 b5)
Open Trace Format support library - development files
otf2-tools (3.0.3-3.1 b1)
Open Trace Format support library - tools
packmol (1:20.14.3-1 b1 [arm64], 1:20.14.3-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Initial configurations for Molecular Dynamics Simulations
paje.app (1.98-1.2)
generic visualization tool (Gantt chart and more)
pal2nal (14.1-3)
converts proteins to genomic DNA alignment
paleomix (1.3.8-2)
pipelines and tools for the processing of ancient and modern HTS data
paml (4.9j dfsg-5 b1 [arm64], 4.9j dfsg-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Phylogenetic Analysis by Maximum Likelihood (PAML)
paraclu (10-1 b1 [arm64, riscv64], 10-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Parametric clustering of genomic and transcriptomic features
parafly (0.1.0-5)
parallel command processing using OpenMP
parallel-fastq-dump (0.6.7-3)
parallel fastq-dump wrapper
parsinsert (1.04-15 b1 [riscv64], 1.04-15 [amd64, arm64, i386, mips64el, ppc64el, s390x])
Parsimonious Insertion of unclassified sequences into phylogenetic trees
parsinsert-testdata (1.04-15)
Test data for parsinsert
parsnp (2.0.6 dfsg-1)
rapid core genome multi-alignment
patman (1.2.2 dfsg-8 b2 [arm64], 1.2.2 dfsg-8 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
rapid alignment of short sequences to large databases
pbbamtools (2.4.0 dfsg-1 b4)
processing Pacific Biosciences binary alignment/map files
pbdagcon (0.3 git20180411.c14c422 dfsg-9)
sequence consensus using directed acyclic graphs
pbhoney (15.8.24 dfsg-8)
genomic structural variation discovery
pbjelly (15.8.24 dfsg-8)
genome assembly upgrading tool
pbsim (1.0.3 git20180330.e014b1d dfsg-3 b1 [arm64, riscv64], 1.0.3 git20180330.e014b1d dfsg-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
simulator for PacBio sequencing reads
pdb-tools (2.5.1-2)
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
perm (0.4.0-8 b2 [arm64], 0.4.0-8 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
efficient mapping of short reads with periodic spaced seeds
persalys (16.1 ds-1 b1 [arm64], 16.1 ds-1 [amd64, mips64el, ppc64el, riscv64, s390x])
GUI for uncertainty treatment and variabilities management
pftools (3.2.12-1)
build and search protein and DNA generalized profiles
phast (1.7 dfsg-1)
phylogenetic analysis with space/time models
phipack (0.0.20160614-5 b1 [arm64, riscv64], 0.0.20160614-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
PHI test and other tests of recombination
phybin (0.3-6 b1 [riscv64], 0.3-6 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
binning/clustering newick trees by topology
phylip (1:3.697 dfsg-4 b1 [arm64], 1:3.697 dfsg-4 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
package of programs for inferring phylogenies
phylonium (1.7-3 b1 [arm64], 1.7-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Fast and Accurate Estimation of Evolutionary Distances
phyml (3:3.3.20220408-4 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 3:3.3.20220408-4 [armel, armhf, i386])
Phylogenetic estimation using Maximum Likelihood
physamp (1.1.0-5 b1 [arm64], 1.1.0-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
sample sequence alignment corresponding to phylogeny
phyutility (2.7.3 dfsg-4 b1 [riscv64], 2.7.3 dfsg-4 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
simple analyses or modifications on both phylogenetic trees and data matrices
phyx (1.3.2 ds-1)
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 b1 [arm64, riscv64], 965-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
SAT solver with proof and core support
pigx-rnaseq (0.1.1-1)
pipeline for checkpointed and distributed RNA-seq analyses
piler (0~20140707-4 b1 [arm64], 0~20140707-4 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
genomic repeat analysis
pilercr (1.06 dfsg-5 b1 [arm64, riscv64], 1.06 dfsg-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
software for finding CRISPR repeats
pilon (1.24-3)
automated genome assembly improvement and variant detection tool
pinfish (0.1.0 ds-4 b3)
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 b1 [arm64, riscv64], 2.0.2 dfsg-12 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [arm64, riscv64], 0.37.3 ds-9 [amd64, mips64el, ppc64el, s390x])
Identifies gene fusions in RNA sequencing data
pkg-r-autopkgtest (20241218)
Script for the automatic testing of R packages
pktools (2.6.7.6 ds-6 b2)
GDAL add-on tools to perform useful raster processing
placnet (1.04-1)
Plasmid Constellation Network project
planetary-system-stacker (0.8.32~git20230901.01f3625-2)
create a sharp image of a planetary system object (moon, sun, planets)
planets (0.1.13-23)
Gravitation simulation of planetary bodies
plasmidid (1.6.5 dfsg-2)
mapping-based, assembly-assisted plasmid identification tool
plasmidseeker (1.3 dfsg-3 b1)
identification of known plasmids from whole-genome sequencing reads
plast (2.3.2 dfsg-10 b5 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 2.3.2 dfsg-10 b3 [riscv64])
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.1-3)
medical image reconstruction and registration
plink (1.07 dfsg-4 b2 [arm64], 1.07 dfsg-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 b3 [riscv64], 2.00~a5.8-231123 dfsg-1 b2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
whole-genome association analysis toolset
pluto-jpl-eph (0.0~git20180228-1.1 b1 [arm64, riscv64], 0.0~git20180228-1.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
command line handling of JPL ephemeres data
pluto-lunar (0.0~git20180825.e34c1d1-1 b1 [amd64, arm64, riscv64], 0.0~git20180825.e34c1d1-1 [armel, armhf, i386, mips64el, ppc64el, s390x])
routines for predictions of positions in solar system
pnetcdf-bin (1.14.0-2)
Programs for reading and writing parallel NetCDF files
poa (2.0 20060928-9 b1 [arm64], 2.0 20060928-9 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Partial Order Alignment for multiple sequence alignment
populations (1.2.33 svn0120106 dfsg-7 b1 [arm64], 1.2.33 svn0120106 dfsg-7 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
population genetic software
porechop (0.2.4 dfsg-6 b1 [arm64], 0.2.4 dfsg-6 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
adapter trimmer for Oxford Nanopore reads
poretools (0.6.0 dfsg-7)
toolkit for nanopore nucleotide sequencing data
poretools-data (0.6.0 dfsg-7)
toolkit for nanopore nucleotide sequencing data -- sample datasets
praat (6.4.25 dfsg-1)
program for speech analysis and synthesis
prank (0.0.170427 dfsg-3 b1 [arm64, riscv64], 0.0.170427 dfsg-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (1.0.11-13 b1)
bayesian estimation of gene trees taking the species tree into account
primer3 (2.6.1-5)
tool to design flanking oligo nucleotides for DNA amplification
primer3-examples (2.6.1-5)
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 (0.603-6)
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 b1 [arm64, riscv64], 1.4-10 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
multiple sequence alignment using partition function posterior probabilities
probcons (1.12-14 b1 [arm64, riscv64], 1.12-14 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
PROBabilistic CONSistency-based multiple sequence alignment
probcons-extra (1.12-14 b1 [arm64, riscv64], 1.12-14 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Extra programs from the probcons package
proda (1.0-14 b1 [arm64], 1.0-14 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
multiple alignment of protein sequences
prodigal (1:2.6.3-6 b1 [arm64, riscv64], 1:2.6.3-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for profbval
profnet-chop (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for profchop
profnet-con (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for profcon
profnet-isis (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for profisis
profnet-md (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for metadisorder
profnet-norsnet (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for norsnet
profnet-prof (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for profacc
profnet-snapfun (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for snapfun
profphd-net (1.0.22-8 b1 [arm64, riscv64], 1.0.22-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
neural network architecture for profphd
profphd-utils (1.0.10-7 b1 [arm64, riscv64], 1.0.10-7 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
profphd helper utilities convert_seq and filter_hssp
proftmb (1.1.12-11 b2 [riscv64], 1.1.12-11 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
per-residue prediction of bacterial transmembrane beta barrels
progressivemauve (1.2.0 4713 dfsg-5 b4 [arm64], 1.2.0 4713 dfsg-5 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
multiple genome alignment algorithms
proj-bin (9.5.1-1)
Cartographic projection library (tools)
prokka (1.14.6 dfsg-6)
rapid annotation of prokaryotic genomes
proteinortho (6.3.1 dfsg-1 b1 [arm64], 6.3.1 dfsg-1 [amd64, ppc64el, riscv64, s390x])
Detection of (Co-)orthologs in large-scale protein analysis
prottest (3.4.2 dfsg-8)
selection of best-fit models of protein evolution
pscan-chip (1.1-3 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.1-3 b2 [riscv64])
ChIP-based identifcation of TF binding sites
pscan-chip-data (1.1-3)
auxiliary data for PScan-ChIP
pscan-tfbs (1.2.2-4 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.2.2-4 b2 [riscv64])
search for transcription factor binding sites
psfex (3.24.2-2)
Point Spread Function model extractor
psortb (3.0.6 dfsg-4 b1)
bacterial localization prediction tool
psychtoolbox-3-common (3.0.19.14.dfsg1-1)
toolbox for vision research -- arch/interpreter independent part
psychtoolbox-3-lib (3.0.19.14.dfsg1-1)
toolbox for vision research -- arch-specific parts
pullseq (1.0.2-5 b1 [arm64], 1.0.2-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Extract sequence from a fasta or fastq
purify (4.1.0-1 b1)
Collection of routines for radio interferometric imaging
pycoqc (2.5.2 dfsg-3)
computes metrics and generates Interactive QC plots
pyensembl (2.3.13-1)
installs data from the Ensembl genome database
pyfai (2024.05-3)
Fast Azimuthal Integration scripts
pyfastx (2.1.0-3)
fast random access to sequences from FASTA/Q file - command
pymca (5.9.3 dfsg-1)
Applications and toolkit for X-ray fluorescence analysis -- scripts
pymca-data (5.9.3 dfsg-1)
Architecture independent data files for PyMca
pymoctool (0.5.2-2)
Python Multi-Order Coverage maps tool for Virtual Observatory
pymol (3.0.0 dfsg-1)
Molecular Graphics System
pymol-data (3.0.0 dfsg-1)
data files for PyMOL
pyomop (4.3.0-1)
OHSDI OMOP Common Data Model tools
pysatellites (2.7-4)
simulates the launching of satellites
python-drizzle-testdata (2.0.0-1)
Dithered image combination for Python (Test data)
python-escript-doc (5.6-10)
Documentation for Escript/Finley
python-pairix-examples (0.3.8-1)
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-2 b8 [arm64], 0.1.1 dfsg-2 b7 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.1.1 dfsg-2 b4 [riscv64])
edit and Hamming distances for biological sequences
python3-bioframe (0.4.1-1)
library to enable flexible, scalable operations on genomic interval dataframes
python3-bornagain (22~git20240726093306.cb41cc4 ds3-2)
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 (2.0.0-3 b3 [arm64], 2.0.0-3 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
cython wrapper for khash-sets/maps, efficient implementation of isin and unique
python3-cyvcf2 (0.31.1-2 b1)
VCF parser based on htslib (Python 3)
python3-datacache (1.4.1-2)
helpers for transparently downloading datasets
python3-datalad-next (1.5.0-1)
DataLad extension for new features and improved user experience
python3-dcmstack (0.9-3)
DICOM to NIfTI conversion - python3 package
python3-deeptools (3.5.5 dfsg-1)
platform for exploring biological deep-sequencing data
python3-deeptoolsintervals (0.1.9-3 b11 [arm64], 0.1.9-3 b10 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.1.9-3 b4 [riscv64])
handlig GTF-like sequence-associated interal-annotation
python3-dials (3.22.1 dfsg3-1)
Diffraction Integration for Advanced Light Sources - Python3
python3-dnapilib (1.1-3)
adapter prediction for small RNA sequencing - library
python3-emperor (1.0.3 ds-9.1)
visualizing high-throughput microbial community data
python3-escript (5.6-10)
Escript/Finley finite elements Python3 system (OpenMP MPI)
python3-escript-mpi (5.6-10)
(OpenMP MPI)
python3-faiss (1.9.0-5 b1)
Python 3 module for efficient similarity search and clustering of dense vectors
python3-geneimpacts (0.3.7-5)
wraps command line tools to assess variants in gene sequences
python3-gfapy (1.2.3 dfsg-3)
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 (0.0.9-3)
is a data integration algorithm
python3-jupyter-sphinx (0.3.2-2)
Jupyter Sphinx Extension - Python3
python3-louvain (0.16-1)
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 (1.6.0-4)
Navigation tool for ARPES data (Python 3)
python3-noise (1.2.3-4 b7 [arm64], 1.2.3-4 b6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 1.2.3-4 b4 [riscv64])
Perlin noise for image generation
python3-onnx (1.16.2-1 b1)
Open Neural Network Exchange (ONNX) (Python)
python3-parmed (4.2.2 dfsg-3 b2 [arm64], 4.2.2 dfsg-3 b1 [amd64, ppc64el])
parameter and topology file editor and molecular mechanical simulator
python3-pdbtools (2.5.1-2)
tools for manipulating and editing PDB files (Python 3 package)
python3-peptidebuilder (1.1.0-3)
generate atomic oligopeptide 3D structure from sequence
python3-pomegranate (0.14.8-7)
Fast, flexible and easy to use probabilistic modelling
python3-prodigy (2.2.5-1)
Protein Binding Affinity Prediction (Python 3)
python3-propka (3.5.1-2)
heuristic pKa calculations with ligands (Python 3)
python3-py2bit (0.3.2-1)
access to 2bit files
python3-pyaml-env (1.2.1-2)
Python3 YAML configuration with environment variables parsing
python3-pybel (0.15.5-1)
Biological Expression Language
python3-pybigwig (0.3.23 dfsg-1 b1)
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 (4.0.3-2)
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-pyobjcryst (2024.2.1-1)
Object-Oriented Crystallographic Library bindings (Python 3)
python3-pyvista (0.44.1-10)
Python3 high-level API to the Visualization Toolkit (VTK)
python3-pyvkfft (2024.1.4 ds1-2)
Binding to the OpenCL backends of VkFFT - Python3
python3-pyvkfft-cuda (2024.1.4 ds1-3) [contrib]
Binding to the CUDA backends of VkFFT - Python3
python3-pyxrd (0.8.4-5)
modeling of X-ray diffraction (XRD) patterns of disordered lamellar structures
python3-seqcluster (1.2.9 ds-4) [contrib]
analysis of small RNA in NGS data
python3-tinyalign (0.2.2-1 b4 [arm64], 0.2.2-1 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
numerical representation of differences between strings
python3-truncnorm (0.0.2-2)
Moments for truncated multivariate normal distributions for Python
(3.8.0-2)
sequence logo generator
python3-xeus-python-shell (0.15.10 ~0.6.1-2)
Native jupyter kernel for python (python library)
python3-xgboost (2.1.3-1)
Scalable and Flexible Gradient Boosting (Python3)
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 (4.15.0-1)
interactive editor for scientific Python
q2templates (2024.5.0 ds-1)
Design template package for QIIME 2 Plugins
qcat (1.1.0-7)
demultiplexing Oxford Nanopore reads from FASTQ files
qcat-examples (1.1.0-7)
demultiplexing Oxford Nanopore reads from FASTQ files (examples)
qcumber (2.3.0-2)
quality control of genomic sequences
qemu-web-desktop (24.07.12 ds1-2)
Remote desktop service with virtual machines in a browser (DARTS).
qfits-tools (6.2.0-9 b1)
FITS manipulation tools
qfitsview (4.2 dfsg-1)
FITS file viewer based on DPUSER
qgis (3.34.13 dfsg-1)
Geographic Information System (GIS)
qgis-api-doc (3.34.13 dfsg-1)
QGIS API documentation
qgis-common (3.34.13 dfsg-1)
QGIS - architecture-independent data
qgis-plugin-grass (3.34.13 dfsg-1)
GRASS plugin for QGIS
qgis-plugin-grass-common (3.34.13 dfsg-1)
GRASS plugin for QGIS - architecture-independent data
qgis-provider-grass (3.34.13 dfsg-1)
GRASS provider for QGIS
qgis-providers (3.34.13 dfsg-1)
collection of data providers to QGIS
qgis-providers-common (3.34.13 dfsg-1)
collection of data providers to QGIS - architecture-independent files
qgis-server (3.34.13 dfsg-1)
QGIS server providing various OGC services
qgis-server-bin (3.34.13 dfsg-1)
QGIS server providing various OGC services (executables)
qgis-server-common (3.34.13 dfsg-1)
QGIS server providing various OGC services (data)
qgis-server-dummy (3.34.13 dfsg-1)
QGIS server providing various OGC services (dummy)
qgis-server-landingpage (3.34.13 dfsg-1)
QGIS server providing various OGC services (landing page)
qgis-server-wcs (3.34.13 dfsg-1)
QGIS server providing various OGC services (WCS)
qgis-server-wfs (3.34.13 dfsg-1)
QGIS server providing various OGC services (WFS)
qgis-server-wfs3 (3.34.13 dfsg-1)
QGIS server providing various OGC services (WFS 3)
qgis-server-wms (3.34.13 dfsg-1)
QGIS server providing various OGC services (WMS)
qgis-server-wmts (3.34.13 dfsg-1)
QGIS server providing various OGC services (WMTS)
qgis3-survex-import (1.3-1)
QGIS3 plugin to read survex 3d files, for cave surveying
qmapshack (1.17.1-1 b5 [amd64], 1.17.1-1 b4 [arm64, armhf], 1.17.1-1 b3 [i386, mips64el])
GPS mapping (GeoTiff and vector) and GPSr management
qmc (0.94-4.1 b1 [arm64, riscv64], 0.94-4.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Quine McClusky Simplification Tool
qrisk2 (0.1.20150729-6)
cardiovascular disease risk calculator
qthid-fcd-controller (4.1-6 b3 [arm64], 4.1-6 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Funcube Dongle controller
qtltools (1.3.1 dfsg-4 b3)
Tool set for molecular QTL discovery and analysis
qttinysa (0.10.6-1)
QT Gui for a tiny SA Spectrum Analyser
quantum-espresso (6.7-3 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 6.7-3 [armhf, i386])
Electronic-Structure and Ab-Initio Molecular Dynamics Suite
quantum-espresso-data (6.7-3)
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 b1 [arm64, riscv64], 2.5-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Neighbor-Joining algorithm for phylogenies
quorum (1.1.2-2 b2 [mips64el, ppc64el, riscv64], 1.1.2-2 b1 [arm64], 1.1.2-2 [amd64])
QUality Optimized Reads of genomic sequences
qutemol (0.4.1~cvs20081111-15 b4 [arm64, mips64el, riscv64], 0.4.1~cvs20081111-15 b3 [amd64, armel, armhf, i386, ppc64el, s390x])
interactive visualization of macromolecules
r-cran-alakazam (1.3.0-1 b1 [arm64, riscv64], 1.3.0-1 [amd64, mips64el, ppc64el, s390x])
Immunoglobulin Clonal Lineage and Diversity Analysis
r-cran-sdmtools (1.1-221.2-1 b2 [arm64], 1.1-221.2-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Species Distribution Modelling Tools
r-cran-shazam (1.2.0-1)
Immunoglobulin Somatic Hypermutation Analysis
r-cran-tigger (1.1.0-1)
Infers new Immunoglobulin alleles from Rep-Seq Data
racon (1.5.0-3 b1 [arm64, riscv64], 1.5.0-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [arm64], 2.3-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Reference-Assisted Genome Ordering UTility
ragout-examples (2.3-5)
Reference-Assisted Genome Ordering UTility (example data)
rambo-k (1.21 dfsg-5)
Read Assignment Method Based On K-mers
rampler (2.1.1-1 b1 [arm64, riscv64], 2.1.1-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
module for sampling genomic sequences
rapmap (0.15.0 dfsg-4 b2)
rapid sensitive and accurate DNA read mapping via quasi-mapping
rapmap-dev (0.15.0 dfsg-4)
rapmap - rapid sensitive and accurate DNA read mapping (some headers)
rapmap-example-data (0.15.0 dfsg-4)
example data for rapmap - rapid sensitive and accurate DNA read mapping
rasmol (2.7.6.0-3 b2 [arm64, riscv64], 2.7.6.0-3 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
visualization of biological macromolecules
raster3d (3.0-7-2 b1)
tools for generating images of proteins or other molecules
rate4site (3.0.0-8 b1 [arm64, riscv64], 3.0.0-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
detector of conserved amino-acid sites
rawtran (1.1-1 b6 [arm64], 1.1-1 b5 [amd64, armel, armhf, i386, mips64el], 1.1-1 b4 [ppc64el, s390x], 1.1-1 b2 [riscv64])
RAW photo to FITS converter
raxml (8.2.13 dfsg-1 b3 [riscv64], 8.2.13 dfsg-1 b2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Randomized Axelerated Maximum Likelihood of phylogenetic trees
ray (2.3.1-9)
de novo genome assemblies of next-gen sequencing data
ray-extra (2.3.1-9)
Scripts and XSL sheets for post-processing for ray
rdp-classifier (2.10.2-7)
extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
readseq (1-15 b1 [arm64], 1-15 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Conversion between sequence formats
reapr (1.0.18 dfsg-7)
universal tool for genome assembly evaluation
recan (0.5 dfsg-1)
genetic distance plotting for recombination events analysis
refmac-dictionary (5.41-3)
dictionary for macromolecular refinement and model building
relion (3.1.3-4 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 3.1.3-4 [armel, armhf, i386])
toolkit for 3D reconstructions in cryo-electron microscopy
relion-gui (3.1.3-4 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 3.1.3-4 [armel, armhf, i386])
toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
repeatmasker-recon (1.08-8 b1 [arm64], 1.08-8 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
finds repeat families from biological sequences
reprof (1.0.1-8)
protein secondary structure and accessibility predictor
resfinder (4.4.2-2)
identify acquired antimicrobial resistance genes
resfinder-db (0.0 git20220524.fa32d9a-1)
ResFinder database is a curated database of acquired resistance genes
resfinder-example (4.4.2-2)
identify acquired antimicrobial resistance genes (example data)
rna-star (2.7.11b dfsg-2 b1)
ultrafast universal RNA-seq aligner
rnahybrid (2.1.2-8 b2 [riscv64], 2.1.2-8 b1 [arm64], 2.1.2-8 [amd64, armhf, i386, mips64el, ppc64el, s390x])
Fast and effective prediction of microRNA/target duplexes
roary (3.13.0 dfsg-2)
high speed stand alone pan genome pipeline
rocketcea (1.2.1-2)
NASA Chemical Equilibrium, wrapped in Python
rockhopper (2.0.3 dfsg2-4)
system for analyzing bacterial RNA-seq data
roguenarok (1.0.1-3 b1 [arm64, riscv64], 1.0.1-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
versatile and scalable algorithm for rogue taxon identification
rsem (1.3.3 dfsg-3 b2 [arm64, riscv64], 1.3.3 dfsg-3 b1 [amd64, mips64el, ppc64el, s390x])
RNA-Seq by Expectation-Maximization
rtax (0.984-8)
Classification of sequence reads of 16S ribosomal RNA gene
ruby-getspg (2.5.0-1 b1)
C library for crystal symmetry determination - Ruby bindings
ruby-rgfa (1.3.1 dfsg-2)
parse, edit and write GFA format graphs in Ruby
runcircos-gui (0.0 git20200528.82dda8c-1 b2 [arm64, riscv64], 0.0 git20200528.82dda8c-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
GUI tool to run circos
sac2mseed (1.13 ds1-1 b2 [arm64], 1.13 ds1-1 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Convert SAC waveform data to MiniSEED
saga (9.7.0 dfsg-1)
System for Automated Geoscientific Analyses
saga-common (9.7.0 dfsg-1)
SAGA GIS architecture independent files
saint (2.5.0 dfsg-4 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 2.5.0 dfsg-4 b2 [riscv64])
Significance Analysis of INTeractome
salmid (0.1.23-5)
rapid Kmer based Salmonella identifier from sequence data
salmon (1.10.2 ds1-1 b4)
wicked-fast transcript quantification from RNA-seq data
samblaster (0.1.26-4 b1 [arm64, riscv64], 0.1.26-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
marks duplicates, extracts discordant/split reads
samclip (0.4.0-4)
filter SAM file for soft and hard clipped alignments
samtools (1.20-3 b1 [arm64], 1.20-3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
processing sequence alignments in SAM, BAM and CRAM formats
samtools-test (1.20-3)
test files for the samtools package
saods9 (8.6 repack-4)
Image display tool for astronomy
saoxmlrpc (8.6 repack-4)
Tcl XML-RPC implementation from SAO
sasview (5.0.6-5)
Small Angle Scattering Analysis suite
sat4j (2.3.5-0.3)
Efficient library of SAT solvers in Java
savi (1.6.0-1 b1 [arm64, riscv64], 1.6.0-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
satellite constellation visualisation
savvy-util (2.1.0-3)
conversion tool for SAV file format
sbmltoolbox (4.1.0-5.1)
libsbml toolbox for octave and matlab
scamp (2.10.0-4)
Compute astrometric and photometric solutions
science-config (1.14.7)
Debian Science Project config package
science-dataacquisition-dev (1.14.7)
Debian Science data acquisition development packages
science-electronics (1.14.7)
Debian Science Electronics transitional package
science-engineering-dev (1.14.7)
Debian Science Engineering-dev packages
science-highenergy-physics (1.14.7)
Debian Science High Energy Physics packages
science-highenergy-physics-dev (1.14.7)
Debian Science High Energy Physics development packages
science-machine-learning (1.14.7)
Debian Science Machine Learning packages
science-mathematics-dev (1.14.7)
Debian Science Mathematics-dev packages
science-meteorology-dev (1.14.7)
Debian Science Meteorology-dev packages
science-nanoscale-physics (1.14.7)
Debian Science Nanoscale Physics packages
science-nanoscale-physics-dev (1.14.7)
Debian Science Nanoscale Physics development packages
science-neuroscience-cognitive (1.14.7)
Debian Science packages for Cognitive Neuroscience
science-neuroscience-modeling (1.14.7)
Debian Science packages for modeling of neural systems
science-physics-dev (1.14.7)
Debian Science Physics-dev packages
science-robotics-dev (1.14.7)
Debian Robotics development packages
science-tasks (1.14.7)
Debian Science tasks for tasksel
science-viewing-dev (1.14.7)
Debian Science development of visualisation applications
scoary (1.6.16-10)
pangenome-wide association studies
scram (0.16.2-3 b3 [arm64], 0.16.2-3 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Probabilistic Risk Analysis Tool
scram-gui (0.16.2-3 b3 [arm64], 0.16.2-3 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
SCRAM GUI front-end
scrappie (1.4.2-8 b7 [amd64, arm64, armhf, i386, mips64el, ppc64el, s390x], 1.4.2-8 b4 [riscv64])
basecaller for Nanopore sequencer
scrm (1.7.4-1 b1 [arm64, riscv64], 1.7.4-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
simulator of evolution of genetic sequences
scythe (0.994 git20141017.20d3cff-5 b1 [arm64], 0.994 git20141017.20d3cff-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Bayesian adaptor trimmer for sequencing reads
seaview (1:5.0.5-2 b2 [arm64, riscv64], 1:5.0.5-2 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Multiplatform interface for sequence alignment and phylogeny
secrecy (0.0.5 ds-4 b1)
tool to handle libsecrecy keys and encrypted files
seer (1.1.4-8 b1)
genomic sequence element (kmer) enrichment analysis
segemehl (0.3.4-5 b2 [arm64, riscv64], 0.3.4-5 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
short read mapping with gaps
sentencepiece (0.2.0-1 b3 [arm64], 0.2.0-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Unsupervised text tokenizer and detokenizer
seq-gen (1.3.4-2 b1 [riscv64], 1.3.4-2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x]) [non-free]
simulate the evolution of nucleotide or amino acid sequences
seqan-apps (2.4.0 dfsg-16 b1 [arm64], 2.4.0 dfsg-16 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
C library for the analysis of biological sequences
seqan-needle (1.0.3 ds-1)
pre-filter for the counting of very large collections of nucleotide sequences
seqan-raptor (3.0.1 ds-5 b1 [arm64, riscv64], 3.0.1 ds-5 [amd64, mips64el, ppc64el])
pre-filter for querying very large collections of nucleotide sequences
seqan-raptor-doc (3.0.1 ds-5)
HTML & PDF documentation for seqan-raptor and its APIs
seqcluster (1.2.9 ds-4) [contrib]
analysis of small RNA in NGS data
seqkit (2.8.2 ds-2)
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqkit-examples (2.8.2 ds-2)
examples for seqkit: toolkit for FASTA/Q file manipulation
seqmagick (0.8.6-3)
imagemagick-like frontend to Biopython SeqIO
seqprep (1.3.2-9 b1 [arm64], 1.3.2-9 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 b1 [arm64, riscv64], 1.4-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
seriation (0.1 git20210125.fc7b8cb-1 b1 [arm64, riscv64], 0.1 git20210125.fc7b8cb-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
finds a suitable linear order for a set of objects
seriation-data (0.1 git20210125.fc7b8cb-1)
test data for seriation
sga (0.10.15-7 b1)
de novo genome assembler that uses string graphs
shapeit4 (4.2.2 dfsg-1 b4 [arm64], 4.2.2 dfsg-1 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
fast and accurate method for estimation of haplotypes (phasing)
shasta (0.12.0-1 b2 [arm64], 0.12.0-1 b1 [amd64])
nanopore whole genome assembly (binaries and scripts)
shelxle (1.0.1552-1 b2 [amd64, arm64, riscv64], 1.0.1552-1 b1 [i386, mips64el, ppc64el, s390x])
graphical user interface for SHELXL
shiny-server (1.5.20.1002-3)
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 b1 [arm64, riscv64], 3.0.7 dfsg-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
comparative genomics tool
sibelia-examples (3.0.7 dfsg-3)
comparative genomics tool (example data)
sibsim4 (0.20-5 b1 [arm64, riscv64], 0.20-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
align expressed RNA sequences on a DNA template
sickle (1.33 git20150314.f3d6ae3-2 b1 [arm64, riscv64], 1.33 git20150314.f3d6ae3-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
windowed adaptive trimming tool for FASTQ files using quality
sightcalibrator (24.1.0-1)
Camera calibration software
sightviewer (24.1.0-1)
DICOM viewer
sigma-align (1.1.3-9 b1 [arm64], 1.1.3-9 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Simple greedy multiple alignment of non-coding DNA sequences
sigviewer (0.6.4-3 b2 [arm64, armel, armhf, riscv64], 0.6.4-3 b1 [amd64, i386, mips64el, ppc64el, s390x])
GUI viewer for biosignals such as EEG, EMG, and ECG
silx (2.1.2 dfsg-1)
Toolbox for X-Ray data analysis - Executables
sim4 (0.0.20121010-8 b1 [arm64, riscv64], 0.0.20121010-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
tool for aligning cDNA and genomic DNA
sim4db (0~20150903 r2013-9)
batch spliced alignment of cDNA sequences to a target genome
simka (1.5.3-8 b2)
comparative metagenomics method dedicated to NGS datasets
simkamin (1.5.3-8)
approximate comparative metagenomics method dedicated to NGS datasets
simrisc (16.02.00-1)
simulation model for breast/lung cancer risk
siril (1.2.4-1)
astronomical image processing tool
siril-common (1.2.4-1)
architecture-independent files for siril
ska (1.0 dfsg-4)
Split Kmer Analysis
skesa (2.4.0-6 b3 [arm64], 2.4.0-6 b2 [amd64])
strategic Kmer extension for scrupulous assemblies
skewer (0.2.2-6 b2 [arm64], 0.2.2-6 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
post-processing of high-throughput DNA sequence reads
skycat (3.1.2 starlink1~b dfsg-9)
Image visualization and access to catalogs and data for astronomy
slang-xfig (0.2.0~.138-1 b1)
produce plots and drawings through Xfig's fig2dev in S-Lang
smalt (0.7.6-13 b1 [arm64], 0.7.6-13 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Sequence Mapping and Alignment Tool
smalt-examples (0.7.6-13)
Sequence Mapping and Alignment Tool (examples)
smiles-scripts (0.2.0 dfsg1-6)
command line tools to handle SMILES descriptors
smithwaterman (0.0 git20160702.2610e25-12 b2)
determine similar regions between two strings or genomic sequences
smrtanalysis (0~20210112)
software suite for single molecule, real-time sequencing
snakemake (7.32.4-6)
pythonic workflow management system
snap (2013-11-29-11 b1 [arm64, riscv64], 2013-11-29-11 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
location of genes from DNA sequence with hidden markov model
snap-aligner (2.0.3 dfsg-2 b1 [arm64], 2.0.3 dfsg-2 [amd64, mips64el, ppc64el, riscv64])
Scalable Nucleotide Alignment Program
snaphu (2.0.7-1) [non-free]
Statistical-Cost, Network-Flow Algorithm for 2D Phase Unwrapping
sniffles (2.2-1)
structural variation caller using third-generation sequencing
snp-sites (2.5.1-2 b2)
Binary code for the package snp-sites
snpomatic (1.0-7 b1 [arm64], 1.0-7 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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-4)
short-read assembly method to build de novo draft assembly
soapsnp (1.03-5 b1 [arm64, riscv64], 1.03-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
resequencing utility that can assemble consensus sequence of genomes
solvate (1.0-3) [non-free]
arranges water molecules around protein structures
solvate-doc (1.0-3) [non-free]
Documentation for solvate
sortmerna (4.3.7-2)
tool for filtering, mapping and OTU-picking NGS reads
source-extractor (2.28.0 ds-2)
Source extractor for astronomical images
sp800-90b-entropy-assessment (1.1.8-3)
Estimating the quality of a source of entropy
spaced (1.2.0-201605 dfsg-4 b1 [arm64], 1.2.0-201605 dfsg-4 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
alignment-free sequence comparison using spaced words
spades (3.15.5 dfsg-8)
genome assembler for single-cell and isolates data sets
spaln (3.0.2 dfsg-2 b1)
splicing-aware transcript-alignment to genomic DNA
spaln-data (3.0.2 dfsg-2)
splicing-aware transcript-alignment to genomic DNA (data)
spass (3.9-1.1 b1 [riscv64], 3.9-1.1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
automated theorem prover for first-order logic with equality
spatialite-bin (5.1.0a-1 b3 [arm64, riscv64], 5.1.0a-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Geospatial extension for SQLite - tools
spd (1.3.0-1.1 b1 [arm64, riscv64], 1.3.0-1.1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Synchrotron image corrections and azimuthal integration
splash (3.11.1-1)
Visualisation tool for Smoothed Particle Hydrodynamics simulation
spoa (4.1.4-2 b1)
SIMD partial order alignment tool
sprai (0.9.9.23 dfsg1-3)
single-pass sequencing read accuracy improver
spread-phy (1.0.7 dfsg-5)
analyze and visualize phylogeographic reconstructions
spview (2.0.2-1)
Spectrum Viewer
sra-toolkit (3.0.9 dfsg-7 b1)
utilities for the NCBI Sequence Read Archive
srst2 (0.2.0-13)
Short Read Sequence Typing for Bacterial Pathogens
ssake (4.0.1-2)
genomics application for assembling millions of very short DNA sequences
ssake-examples (4.0.1-2)
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 (1.1-15 b1)
Smith-Waterman aligner based on libssw
stacks (2.68 dfsg-1)
pipeline for building loci from short-read DNA sequences
staden (2.0.0 b11-5 b1 [arm64], 2.0.0 b11-5 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
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 (1.15.0-1.1)
programs for manipulating DNA sequencing files (usage examples)
staden-io-lib-utils (1.15.0-1.1 b2)
programs for manipulating DNA sequencing files
stardata-common (0.8 nmu1 b1 [riscv64], 0.8 nmu1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Common framework to manage astronomy packages
starpu-contrib-examples (1.4.5 dfsg-2 b2) [contrib]
Task scheduler for heterogeneous multicore machines - exs
starpu-examples (1.4.5 dfsg-4 b1)
Task scheduler for heterogeneous multicore machines - exs
stellarium (24.3-1)
real-time photo-realistic sky generator
stellarium-data (24.3-1)
Stellarium data files
step (4:22.12.3-1 b4 [riscv64], 4:22.12.3-1 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
interactive physical simulator for KDE
stiff (2.4.0-7 b2 [arm64], 2.4.0-7 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
convert scientific FITS images to the TIFF format
stilts (3.5.1-2)
Starlink Tables Infrastructure Library Tool Set
stringtie (2.2.1 ds-3 b2 [arm64], 2.2.1 ds-3 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
assemble short RNAseq reads to transcripts
subarch-select (0.2-1)
Select among binaries based upon x86 microarchitecture support
subread (2.0.7 dfsg-1)
toolkit for processing next-gen sequencing data
subread-data (2.0.7 dfsg-1)
data files for subread package
suitename (0.4.130509 git20210223.ebb1325-1 b1 [arm64, riscv64], 0.4.130509 git20210223.ebb1325-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
categorize each suite in an RNA backbone
sumo (1.18.0 dfsg-4)
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 (1.4.14-2)
cave surveying and mapping software
survex-aven (1.4.14-2)
sophisticated cave survey viewer for Survex
survivor (1.0.7-4 b1 [riscv64], 1.0.7-4 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
tool set for simulating/evaluating SVs
svim (2.0.0-3)
Structural variant caller for long sequencing reads
swarm (3.1.5 dfsg-2 b1 [arm64], 3.1.5 dfsg-2 [amd64, ppc64el])
robust and fast clustering method for amplicon-based studies
swarp (2.41.5-1 b4 [arm64], 2.41.5-1 b3 [amd64, armel, armhf, i386, mips64el, s390x], 2.41.5-1 b2 [ppc64el, riscv64])
Resample and co-add together FITS images
swe-standard-data (4.0-20221111-2)
Swiss Ephemeris library (standard set of ephemeris files).
sweed (3.2.1 dfsg-6)
assessment of SNPs for their evolutionary advantage
t-coffee (13.45.0.4846264 really13.41.0.28bdc39 dfsg-1 b1 [arm64, riscv64], 13.45.0.4846264 really13.41.0.28bdc39 dfsg-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 (1.20 ds-2)
generic indexer for TAB-delimited genome position files
tandem-mass (1:201702011-1 b1 [amd64, riscv64], 1:201702011-1 [arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
mass spectrometry software for protein identification
tantan (51-1)
low complexity and tandem repeat masker for biosequences
tclfitsy (8.6 repack-4)
Tcl FITS Extension
terraintool (1.19-1)
Generates survex/therion terrain models from SRTM/NASADEM data.
theli (3.1.4-2)
Astronomical image data reduction pipeline
therion (6.3.1-2)
Cave surveying - 2D and 3D drawing software
therion-viewer (6.3.1-2)
Cave surveying - 3D viewer for therion models
theseus (3.3.0-14 b1)
superimpose macromolecules using maximum likelihood
theseus-examples (3.3.0-14)
superimpose macromolecules using maximum likelihood (examples)
thesias (3.1.1-3)
Testing Haplotype Effects In Association Studies
threeb (0.0~git20220106110332.a3144e0-6 b2 [riscv64], 0.0~git20220106110332.a3144e0-6 b1 [amd64, i386, s390x], 0.0~git20220106110332.a3144e0-6 [armel, armhf])
3B Microscopy Analysis Software - command-line tool
threeb-imagej (0.0~git20220106110332.a3144e0-6 b2 [riscv64], 0.0~git20220106110332.a3144e0-6 b1 [amd64, i386, s390x], 0.0~git20220106110332.a3144e0-6 [armel, armhf])
3B Microscopy Analysis Software - ImageJ plugin
tiddit (3.6.1 dfsg-1 b4 [arm64], 3.6.1 dfsg-1 b3 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64])
structural variant calling
tigr-glimmer (3.02b-6 b2 [arm64], 3.02b-6 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Gene detection in archea and bacteria
timbl (6.9-2 b1)
Tilburg Memory Based Learner
timblserver (1.18-3 b1)
Server extensions for Timbl
tiny-dnn (1.0.0a3 ds-4)
header only deep learning framework in C
tippecanoe (2.53.0-1 b1 [arm64], 2.53.0-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
build vector tilesets from large collections of GeoJSON features
tksao (8.6 repack-4)
Tk widgets for astronomical imaging and data visualization
tm-align (20190822 dfsg-3)
structural alignment of proteins
tnseq-transit (3.3.4-1)
statistical calculations of essentiality of genes or genomic regions
tombo (1.5.1-7)
identification of modified nucleotides from raw nanopore sequencing data
topcat (4.10.2-1)
Tool for OPerations on Catalogues And Tables
tophat-recondition (1.4-3)
post-processor for TopHat unmapped reads
topp (2.6.0 cleaned1-4 b4)
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 dfsg1-1 b3 [arm64, riscv64], 1.5.3 dfsg1-1 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Top-down proteoform identification and characterization (programs)
toppic-common (1.5.3 dfsg1-1)
Top-down proteoform identification and characterization (common data)
toppred (1.10-10 b1 [arm64, riscv64], 1.10-10 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
transmembrane topology prediction
tortoize (2.0.11-1 b2 [riscv64], 2.0.11-1 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [arm64, riscv64], 3.0.6~beta dfsg-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
interpretation of DNA Sanger sequencing data
transdecoder (5.7.1-2)
find coding regions within RNA transcript sequences
transfuse (0.5.8-1 b5 [arm64], 0.5.8-1 b4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.5.8-1 b3 [riscv64])
Runs formatted documents through transformations/translation
transrate-tools (1.0.0-5 b1 [riscv64], 1.0.0-5 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
helper for transrate
transtermhp (2.09-5 b1 [arm64, riscv64], 2.09-5 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
find rho-independent transcription terminators in bacterial genomes
travis (220729-1 b1 [arm64, riscv64], 220729-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
trajectory analyzer and visualizer
tree-ppuzzle (5.3~rc16 dfsg-12 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 5.3~rc16 dfsg-12 [armel, armhf, i386])
Parallelized reconstruction of phylogenetic trees by maximum likelihood
tree-puzzle (5.3~rc16 dfsg-12 b1 [amd64, arm64, mips64el, ppc64el, riscv64, s390x], 5.3~rc16 dfsg-12 [armel, armhf, i386])
Reconstruction of phylogenetic trees by maximum likelihood
treeview (1.2.0 dfsg-2)
Java re-implementation of Michael Eisen's TreeView
treeviewx (0.5.1 git20100823.7e4d0e9-4 b5 [arm64, mips64el], 0.5.1 git20100823.7e4d0e9-4 b4 [amd64, armel, armhf, i386, ppc64el, s390x], 0.5.1 git20100823.7e4d0e9-4 b3 [riscv64])
Displays and prints phylogenetic trees
trf (4.09.1-6 b1 [arm64, riscv64], 4.09.1-6 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
locate and display tandem repeats in DNA sequences
trf-examples (4.09.1-6)
locate and display tandem repeats in DNA sequences (examples)
triangle-bin (1.6-6) [non-free]
High-quality 2-D mesh generator -- binary programs
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 b2 [arm64], 0.96 dfsg-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
toolkit to carry out genetic association for multi-category phenotypes
trinityrnaseq (2.15.2 dfsg-1)
RNA-Seq De novo Assembly
trinityrnaseq-examples (2.15.2 dfsg-1)
RNA-Seq De novo Assembly common example and testing files
trnascan-se (2.0.12 ds-1) [non-free]
detection of transfer RNA genes in genomic sequence
trnascan-se-common (2.0.12 ds-1) [non-free]
detection of transfer RNA genes in genomic sequence (common files)
tunnelx (20190701-1)
Cave Survey drawing software
tvc (5.0.3 git20151221.80e144e dfsg-5 b3)
genetic variant caller for Ion Torrent sequencing platforms
twms (0.07z git20201202 bb7c3f8-2.1)
tiny web map service
twopaco (1.0.0 dfsg-1 b1 [arm64, riscv64], 1.0.0 dfsg-1 [amd64, armhf, i386, mips64el, ppc64el, s390x])
build the compacted de Bruijn graph from many complete genomes
uc-echo (1.12-19 b1 [arm64], 1.12-19 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
error correction algorithm designed for short-reads from NGS
ucto (0.30-3 b1)
Unicode Tokenizer
uctodata (0.9.1-1)
Data files for Ucto
ucx-utils (1.17.0 ds-3)
Utilities for the UCX messaging library
ugene (51.0 dfsg-2)
integrated bioinformatics toolkit
ugene-data (51.0 dfsg-2)
required data for UGENE - integrated bioinformatics toolkit
uhd-doc (4.7.0.0 ds1-2)
universal hardware driver for Ettus Research products - doc
uhd-host (4.7.0.0 ds1-2 b2)
universal hardware driver for Ettus Research products - host apps
umis (1.0.9-2)
tools for processing UMI RNA-tag data
umis-examples (1.0.9-2)
tools for processing UMI RNA-tag data (examples)
uncalled (2.3 ds-3 b1)
Utility for Nanopore Current Alignment to Large Expanses of DNA
unicycler (0.5.1 dfsg-1.1)
hybrid assembly pipeline for bacterial genomes
unicycler-data (0.5.1 dfsg-1.1)
hybrid assembly pipeline for bacterial genomes (data package)
unifrac-tools (1.4-3 b4)
high-performance phylogenetic diversity calculations (binaries)
unihedron-device-manager (1.0.0.337-1 b1)
Unihedron Device manager (UDM)
unikmer (0.20.0-1 b3)
Toolkit for nucleic acid k-mer analysis
units-filter (4.2.1-1 b2 [riscv64], 4.2.1-1 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Parser for expressions concerning physical values
units-master (4.2.1-1)
Powerful units converter with a GUI
varna (3-93 ds-7)
Visualization Applet for RNA
varscan (2.4.3 dfsg-4) [non-free]
variant detection in next-generation sequencing data
vcfanno (0.3.5 ds-2 b3)
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 b2 [arm64], 0.1.16-3 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Collection of tools to work with VCF files
vdjtools (1.2.1 git20190311 repack-2) [non-free]
framework for post-analysis of B/T cell repertoires
velvet (1.2.10 dfsg1-9)
Nucleic acid sequence assembler for very short reads
velvet-example (1.2.10 dfsg1-9)
Example data for the Velvet sequence assembler
velvet-long (1.2.10 dfsg1-9)
Nucleic acid sequence assembler for very short reads, long version
velvet-tests (1.2.10 dfsg1-9)
Test data for the Velvet sequence assembler
velvetoptimiser (2.2.6-5)
automatically optimise Velvet do novo assembly parameters
veryfasttree (4.0.4 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
vienna-rna (2.6.4 dfsg-1 b1 [s390x], 2.6.4 dfsg-1 [amd64, arm64, armel, armhf, mips64el, ppc64el, riscv64]) [non-free]
RNA sequence analysis
virulencefinder (2.0.5-2)
identify virulence genes in total or partial sequenced isolates of bacteria
virulencefinder-examples (2.0.5-2)
example data for virulencefinder
visp-images-data (3.6.0-1)
visual servoing library - dataset reference files
vitables (3.0.2-4)
graphical tool to browse and edit PyTables and HDF5 files
vmatch (2.3.1 dfsg-9 b1 [arm64, riscv64], 2.3.1 dfsg-9 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
large scale sequence analysis software
voro (0.5 revert-to-0.4.6 dfsg1-1 b1 [arm64, riscv64], 0.5 revert-to-0.4.6 dfsg1-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [arm64, riscv64], 1.22.3149-2 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Voronoi diagram-based tool to find atom contacts
votca (2024.1-1)
Molecular dynamics analysis - coarse-graining and charge transport
votca-data (2024.1-1)
VOTCA molecular dynamics analysis - basis sets and scripts
votca-tutorials (2024.1-1)
VOTCA molecular dynamics analysis - tutorials
vsearch (2.29.1-1 b1)
tool for processing metagenomic sequences
vsearch-examples (2.29.1-1)
Test Data for vsearch tool for processing metagenomic sequences
vt (0.57721 ds-3 b2 [arm64, riscv64], 0.57721 ds-3 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
toolset for short variant discovery in genetic sequence data
vt-examples (0.57721 ds-3)
toolset for short variant discovery in genetic sequence data (examples)
wannier90 (3.1.0 ds-10)
Maximally Localized Wannier Functions - executables
wannier90-data (3.1.0 ds-10)
Maximally Localized Wannier Functions - documentation and examples
wcslib-tools (8.4 ds-1)
Command line tools utilizing wcslib
wcstools (3.9.7-1.1 b1)
Handle the WCS of a FITS image
weightwatcher (1.12 dfsg-3 b1 [arm64, riscv64], 1.12 dfsg-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [arm64, riscv64], 0.1.5-8 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Wisconsin's High-Throughput Alignment Method
wigeon (20101212 dfsg1-6)
reimplementation of the Pintail 16S DNA anomaly detection utility
wise (2.4.1-25)
comparison of biopolymers, like DNA and protein sequences
wsclean (3.4-3 b2)
Fast generic widefield interferometric imager
wtdbg2 (2.5-10)
de novo sequence assembler for long noisy reads
wtdbg2-examples (2.5-10)
Examples for wtdbg - de novo sequence assembler
wxastrocapture (1.8.1 git20140821.796e1a1 dfsg-2 b5 [mips64el], 1.8.1 git20140821.796e1a1 dfsg-2 b4 [amd64, arm64, armel, armhf, i386, ppc64el, s390x], 1.8.1 git20140821.796e1a1 dfsg-2 b3 [riscv64])
Windows linuX Astronomy Capture
x13as (1.1-b61-1) [non-free]
seasonal adjustment software for modeling time series
xbs (0-12)
3-d models and movies of molecules
xcas (1.9.0.93 dfsg2-3)
Computer Algebra System - console and graphical calculator
xcrysden (1.6.2-4 b1 [arm64, riscv64], 1.6.2-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
Crystalline and Molecular Structure Visualizer
xcrysden-data (1.6.2-4)
Crystalline and Molecular Structure Visualizer (Data Files)
xdrawchem (1:1.11.1-2)
Chemical structures and reactions editor
xeus-python-dev (0.15.10 ~0.6.1-2 b3 [arm64], 0.15.10 ~0.6.1-2 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Native jupyter kernel for python (headers)
xfoil (6.99.dfsg 1-3 b2 [arm64], 6.99.dfsg 1-3 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
program for the design and analysis of subsonic airfoils
xgterm (2.2~rc1 dfsg-5)
Terminal emulator to work with IRAF
ximtool (2.2~rc1 dfsg-5)
Interactive image display program for the X Window System
xmds2 (3.1.0 dfsg2-10)
eXtensible Multi-Dimensional Simulator
xmpsolve (3.2.1-10.1 b2)
Multiprecision polynomial solver (graphical version)
xpa-tools (2.1.20-3)
Tools for seamless communication between Unix programs
xplot (1.19-9.1 b2 [riscv64], 1.19-9.1 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
simple on-screen x-y column data plotter
xplot-xplot.org (0.90.7.1-4 b1 [amd64, arm64, riscv64], 0.90.7.1-4 [armel, armhf, i386, mips64el, ppc64el, s390x])
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 b1 [riscv64], 6.11b 1.dfsg-1.1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
Phase Plane Plus Auto: Solves many kinds of equations
xpython (0.15.10 ~0.6.1-2 b3 [arm64], 0.15.10 ~0.6.1-2 b2 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
Native jupyter kernel for python (binary)
xtb (6.7.0-1 b1 [arm64], 6.7.0-1 [amd64, armhf, i386, mips64el, ppc64el, riscv64, s390x])
semiempirical extended tight-binding program package
xyscan (4.66-1 b1 [arm64], 4.66-1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
data thief for scientists
yade (2024.08a-4 b1)
Platform for discrete element modeling
yaha (0.1.83-3 b1 [arm64, riscv64], 0.1.83-3 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
find split-read mappings on single-end queries
yale (5.0.95-3) [non-free]
stellar data set from the Yale Bright Star Catalog
yanagiba (1.0.0-5)
filter low quality Oxford Nanopore reads basecalled with Albacore
yanosim (0.1-6)
read simulator nanopore DRS datasets
yorick (2.2.04 dfsg1-14)
interpreted language and scientific graphics
yorick-av (0.0.6-1 b3 [amd64, arm64, armel, armhf, i386, mips64el, ppc64el, s390x], 0.0.6-1 b2 [riscv64])
write movies from Yorick in various formats
yorick-cubeview (2.2-2.2)
3D FITS data viewer specialized in spectro-imaging
yorick-curses (0.1-7)
interface to the (n)curses library for the Yorick language
yorick-data (2.2.04 dfsg1-14)
interpreted library for the Yorick language
yorick-dev (2.2.04 dfsg1-14)
development files for the Yorick interpreted language
yorick-full (2.2.04 dfsg1 full b1 [amd64, riscv64], 2.2.04 dfsg1 full [arm64, armel, armhf, i386, mips64el, ppc64el, s390x])
full installation of the Yorick interpreter and add-ons
yorick-gl (1.1 cvs20070922 dfsg-7)
OpenGL 3D graphics support for the Yorick language
yorick-gy (0.0.5-3)
GObject introspection and Gtk bindings for Yorick
yorick-gyoto (2.0.2-5)
General relativistic geodesic integration for the Yorick language
yorick-hdf5 (0.8.0-9 b1)
Hierarchical Data Format 5 interface for the Yorick language
yorick-imutil (0.5.7-4)
fast image manipulation routines for the Yorick language
yorick-mira (1.1.0 git20170124.3bd1c3~dfsg1-2)
optical interferometry image reconstruction within Yorick
yorick-ml4 (0.6.0-6)
Matlab file format support for the Yorick language
yorick-mpeg (0.1-4 b1 [arm64, riscv64], 0.1-4 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
MPEG output support for the Yorick language
yorick-optimpack (1.3.2 dfsg 1.4.0-1 b1 [arm64, riscv64], 1.3.2 dfsg 1.4.0-1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
optimization of large scale problems for the Yorick language
yorick-soy (1.4.0-3 b2 [arm64], 1.4.0-3 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, riscv64, s390x])
sparse matrix operations for the Yorick language
yorick-svipc (0.16-7 b1)
interprocess communication (shared memory...) for Yorick
yorick-yeti (6.4.0-2)
utility plugin for the Yorick language
yorick-yeti-fftw (6.4.0-2)
FFT plugin for the Yorick language
yorick-yeti-regex (6.4.0-2)
POSIX regular expressions for the Yorick language
yorick-yeti-tiff (6.4.0-2)
TIFF image format input for the Yorick language
yorick-ygsl (1.2.1-1 b6 [mips64el], 1.2.1-1 b4 [amd64, arm64, armel, armhf, i386, ppc64el, s390x], 1.2.1-1 b2 [riscv64])
GSL special functions plugin for the Yorick language
yorick-ynfft (1.0.4-2)
nonequispaced fast Fourier transform for Yorick
yorick-yutils (1.5.2-2)
various utilities for the Yorick language
yorick-z (1.2.0 cvs20080115-5.1 b2 [arm64, mips64el, riscv64], 1.2.0 cvs20080115-5.1 b1 [amd64, armel, armhf, i386, ppc64el, s390x])
zlib, jpeg and png support for the Yorick language
z3 (4.13.3-1)
theorem prover from Microsoft Research
z88 (15 dfsg-1)
Finite Element Analysis Program - runtime
z88-data (15 dfsg-1)
Finite Element Analysis Program - data
zegrapher (3.1.1-4 b2 [arm64, riscv64], 3.1.1-4 b1 [amd64, armel, armhf, i386, mips64el, ppc64el, s390x])
plotting mathematical functions and sequences on the plane
zfp (1.0.1-4 b3)
Fixed-Rate Compressed Floating-Point Arrays - binary programs
ztex-bmp (20120314-2 b1 [amd64, arm64, armel, armhf, i386], 20120314-2 [ppc64el])
universal macro processor