Software Packages in "forky", Subsection science

3depict (0.0.23-2+b7 [armhf], 0.0.23-2+b6 [arm64, riscv64], 0.0.23-2+b5 [amd64, i386, ppc64el, s390x], 0.0.23-2+b1 [loong64])

visualisation and analysis for single valued point data

abacas (1.3.1-10)

close gaps in genomic alignments from short reads

abacas-examples (1.3.1-10)

sample data for abacas to close gaps in genomic alignments

abpoa (1.5.6-1+b1)

adaptive banded Partial Order Alignment

abyss (2.3.10-2)

de novo, parallel, sequence assembler for short reads

achilles (3-1)

Artificial life and evolution simulator

adapterremoval (2.3.4-1+b1 [arm64, loong64], 2.3.4-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

adapterremoval-examples (2.3.4-1)

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

adms (2.3.7-2+b1)

Automatic device model synthesizer for Verilog-AMS

adun-core (0.81-15+b2 [arm64], 0.81-15+b1 [amd64, armhf, i386, ppc64el, riscv64, s390x], 0.81-15 [loong64])

Molecular Simulator

aegean (0.16.0+dfsg-5+b1 [arm64, loong64], 0.16.0+dfsg-5 [amd64, armhf, i386, ppc64el, s390x])

integrated genome analysis toolkit

aevol (9.4.0-1)

digital genetics model to run Evolution Experiments in silico

aghermann (1.1.2-5+b4 [arm64, riscv64], 1.1.2-5+b3 [amd64, armhf, i386, ppc64el, s390x], 1.1.2-5+b1 [loong64])

Sleep-research experiment manager

aladin (12.060+dfsg-4)

Interactive sky atlas for astronomical images and datasets

alfa (2.2-1+b4 [arm64], 2.2-1+b2 [amd64, armhf, i386, ppc64el, riscv64, s390x], 2.2-1+b1 [loong64])

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 (4.3.0-4)

NGS copy number algorithms

altree (1.3.2-4+b1 [loong64], 1.3.2-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

program to perform phylogeny-based association and localization analysis

altree-examples (1.3.2-4)

example files for ALTree

amap-align (2.2+git20080214.600fc29+dfsg-2+b2 [arm64], 2.2+git20080214.600fc29+dfsg-2+b1 [loong64, riscv64], 2.2+git20080214.600fc29+dfsg-2 [amd64, armhf, i386, ppc64el, s390x])

Protein multiple alignment by sequence annealing

ampliconnoise (1.29-17+b1 [arm64], 1.29-17 [amd64, armhf, i386, ppc64el, riscv64, s390x])

removal of noise from 454 sequenced PCR amplicons

andi (0.14-3+b2 [arm64], 0.14-3+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Efficient Estimation of Evolutionary Distances

ants (2.6.4+dfsg-1)

advanced normalization tools for brain and image analysis

any2fasta (0.8.1-1)

convert various sequence formats to FASTA

any2fasta-examples (0.8.1-1)

convert various sequence formats to FASTA (example data)

aoflagger (3.5.1-2)

Find RFI in radio astronomical observations

apache-arrow-testing (0.0+git20260310-2)

data for testing the apache-arrow suite

apache-parquet-testing (0.0+git20260304-2)

data for testing the apache-arrow suite

apbs (3.4.1-7+b1)

Adaptive Poisson Boltzmann Solver

apbs-data (3.4.1-7)

data files for APBS (Adaptive Poisson Boltzmann Solver)

apbs-doc (3.4.1-7)

Adaptive Poisson Boltzmann Solver

apertium-af-nl (0.3.0-3)

Transitional dummy package for apertium-afr-nld

apertium-afr-nld (0.3.0-3)

Apertium translation data for the Afrikaans-Dutch pair

apertium-all-dev (3.8.1-3)

Metapackage for all tools required for Apertium development

apertium-anaphora (1.1.1-1+b6 [arm64], 1.1.1-1+b4 [amd64, armhf, i386, ppc64el, riscv64, s390x], 1.1.1-1+b1 [loong64])

Anaphora resolution module for Apertium

apertium-apy (0.13.0-2)

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 (3.9.12-2)

Development tools and library for Apertium

apertium-eng-cat (1.0.1-5)

Apertium translation data for the English-Catalan pair

apertium-eng-spa (0.8.1-3)

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 (1.1.1-3)

Transitional dummy package for apertium-spa-ast

apertium-es-it (0.2.1-3)

Transitional dummy package for apertium-spa-ita

apertium-eval-translator (1.2.2-1)

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 (1.0.2-1)

Helper for Apertium and Giellatekno languages and pairs

apertium-hbs-eng (0.5.1-2)

Apertium translation data for the Serbo-Croatian - English pair

apertium-hbs-mkd (0.1.1-2)

Apertium translation data for the Serbo-Croatian-Macedonian pair

apertium-hbs-slv (0.5.1-2)

Apertium translation data for the Serbo-Croatian-Slovenian pair

apertium-hin (0.1.0~r59158-4)

Apertium single language data for Hindi

apertium-id-ms (0.1.2-3)

Transitional dummy package for apertium-ind-zlm

apertium-ind-zlm (0.1.2-3)

Apertium translation data for the Indonesian-Malay pair

apertium-is-sv (0.1.1-3)

Transitional dummy package for apertium-isl-swe

apertium-isl-swe (0.1.1-3)

Apertium translation data for the Icelandic-Swedish pair

apertium-lex-tools (0.5.0-1+b3)

Constraint-based lexical selection module

apertium-lex-tools-dev (0.5.0-1+b3)

Development library for Apertium lexical selection module

apertium-mk-bg (0.2.1-3)

Transitional dummy package for apertium-mkd-bul

apertium-mk-en (0.1.3-3)

Transitional dummy package for apertium-mkd-eng

apertium-mkd-bul (0.2.1-3)

Apertium translation data for the Macedonian-Bulgarian pair

apertium-mkd-eng (0.1.3-3)

Apertium translation data for the Macedonian-English pair

apertium-nno-nob (1.6.0-1)

Apertium translation data for the Norwegian Nynorsk-Norwegian Bokmål pair

apertium-oci-fra (1.0.0-2)

Apertium translation data for the Occitan-French pair

apertium-oci-spa (1.0.9-2)

Apertium translation data for the Occitan (post 1500)-Spanish 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 (1.2.2-1)

Apertium recursive structural transfer module

apertium-regtest (0.9.2-3)

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 (0.7.1-1+b2 [arm64], 0.7.1-1+b1 [amd64, armhf, i386, loong64, 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 (1.1.1-3)

Apertium translation data for the Spanish-Asturian pair

apertium-spa-ast

virtual package provided by apertium-spa-ast

apertium-spa-cat (2.2.0-3)

Apertium translation data for the Spanish-Catalan pair

apertium-spa-ita (0.2.1-3)

Apertium translation data for the Spanish-Italian pair

apertium-srd-ita (1.3.0-1)

Apertium translation data for the Sardinian-Italian pair

apertium-swe-dan (0.8.1-3)

Apertium translation data for the Swedish-Danish pair

apertium-swe-nor (0.4.0-1)

Apertium translation data for the Swedish-Norwegian pair

apertium-urd (0.1.0~r61311-3)

Apertium single language data for Urdu

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

Apertium translation data for the Urdu-Hindi pair

aragorn (1.2.41-3+b2 [arm64], 1.2.41-3+b1 [loong64], 1.2.41-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

tRNA and tmRNA detection in nucleotide sequences

arden (1.0-6)

specificity control for read alignments using an artificial reference

ariba (2.14.7+ds-12)

Antibiotic Resistance Identification By Assembly

art-nextgen-simulation-tools (20160605+dfsg-5+b2 [arm64, riscv64], 20160605+dfsg-5+b1 [amd64, armhf, i386, loong64, 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-5)

genome browser and annotation tool

artfastqgenerator (0.0.20150519-6)

outputs artificial FASTQ files derived from a reference genome

artfastqgenerator-examples (0.0.20150519-6)

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

asdftool (5.2.0-1)

Command line tool to manipulate ASDF scientific data files

ase (3.26.0-3)

Atomic Simulation Environment

assembly-stats (1.0.1+ds-8+b1 [amd64, arm64, loong64], 1.0.1+ds-8 [armhf, i386, ppc64el, riscv64, 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 (2024.11.13-1)

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

astap-cli (2025.10.08-1)

astrometric (plate) solver, command line version

astro-tasks (5.0)

Debian Astronomy Pure Blend (tasksel tasks)

astromatic (1.3)

Astronomical pipeline software collection

astrometry-data-2mass (1.2) [contrib]

Astrometry.net 2MASS index files downloader

astrometry-data-2mass-00 (1.2) [contrib]

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

astrometry-data-2mass-01 (1.2) [contrib]

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

astrometry-data-2mass-02 (1.2) [contrib]

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

astrometry-data-2mass-03 (1.2) [contrib]

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

astrometry-data-2mass-04 (1.2) [contrib]

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

astrometry-data-2mass-05 (1.2) [contrib]

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

astrometry-data-2mass-06 (1.2) [contrib]

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

astrometry-data-2mass-07 (1.2) [contrib]

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

astrometry-data-2mass-08-19 (1.2) [contrib]

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

astrometry-data-tycho2 (2-5)

Astrometry.net Tycho-2 index files

astrometry-data-tycho2-07 (2-5+b1)

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

astrometry-data-tycho2-07-bigendian (2-5)

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

astrometry-data-tycho2-07-littleendian (2-5)

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

astrometry-data-tycho2-08 (2-5+b1)

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

astrometry-data-tycho2-08-bigendian (2-5)

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

astrometry-data-tycho2-08-littleendian (2-5)

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

astrometry-data-tycho2-09 (2-5+b1)

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

astrometry-data-tycho2-09-bigendian (2-5)

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

astrometry-data-tycho2-09-littleendian (2-5)

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

astrometry-data-tycho2-10-19 (2-5+b1)

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

astrometry-data-tycho2-10-19-bigendian (2-5)

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

astrometry-data-tycho2-10-19-littleendian (2-5)

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

astrometry.net (0.98+dfsg-1+b2)

Astrometry plate solver

astronomical-almanac (5.6-9+b1 [arm64, loong64], 5.6-9 [amd64, armhf, i386, ppc64el, riscv64, s390x])

astronomical almanac - calculate planet and star positions

astropy-utils (7.2.0-1)

Command line tools from astropy

atac (0~20150903+r2013-10+b2)

genome assembly-to-assembly comparison

ataqv (1.3.1+ds-4)

ATAC-seq QC and visualization

atomes (1.2.1-1+b2 [arm64, loong64], 1.2.1-1+b1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

atomic-scale 3D modeling toolbox

atomes-data (1.2.1-1)

atomic-scale 3D modeling toolbox (data)

atropos (1.1.32+dfsg-2+b3 [amd64, arm64, armhf, i386, ppc64el, riscv64], 1.1.32+dfsg-2+b1 [loong64])

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

augur (24.4.0-3)

pipeline components for real-time virus analysis

augustus (3.5.0+dfsg-5+b3 [arm64], 3.5.0+dfsg-5+b2 [amd64, armhf, i386, ppc64el, riscv64, s390x], 3.5.0+dfsg-5+b1 [loong64])

gene prediction in eukaryotic genomes

augustus-data (3.5.0+dfsg-5)

data files for AUGUSTUS

autodock (4.2.6-9+b3 [arm64], 4.2.6-9+b2 [riscv64], 4.2.6-9+b1 [loong64], 4.2.6-9 [amd64, armhf, i386, 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 (1.2.7-3+b1)

docking of small molecules to proteins

autogrid (4.2.6-9+b3 [arm64], 4.2.6-9+b2 [riscv64], 4.2.6-9+b1 [loong64], 4.2.6-9 [amd64, armhf, i386, ppc64el, s390x])

pre-calculate binding of ligands to their receptor

autogrid-test (4.2.6-9)

test files for AutoGrid

avce00 (2.0.0-10+b1 [arm64, loong64], 2.0.0-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Conversion of ESRI Arcinfo Vector Coverage in E00 format

avogadro (1.101.0-1+b1 [arm64, loong64], 1.101.0-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Molecular Graphics and Modelling System

avogadro-utils (1.101.0-6)

Molecular Graphics and Modelling System (library)

axe-demultiplexer (0.3.3+dfsg-5+b1 [arm64, loong64], 0.3.3+dfsg-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Trie-based DNA sequencing read demultiplexer

bagel (1.2.2-8+b1)

Computational Chemistry Package

baitfisher (1.2.7+git20211020.de26d5c+dfsg-2+b1 [arm64, loong64], 1.2.7+git20211020.de26d5c+dfsg-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

software package for designing hybrid enrichment probes

bali-phy (4.1+dfsg-1+b1 [amd64, arm64, i386, ppc64el, riscv64, s390x], 4.1+dfsg-1 [loong64])

Bayesian Inference of Alignment and Phylogeny

ballview (1.5.0+git20220524.d85d2dd-5)

free molecular modeling and molecular graphics tool

bamclipper (1.0.0-3)

Remove gene-specific primer sequences from SAM/BAM alignments

bamkit (0.0.1+git20170413.ccd079d-3)

tools for common BAM file manipulations

bamtools (2.5.3+dfsg-2)

toolkit for manipulating BAM (genome alignment) files

bandage (0.9.0-2+b3 [arm64, riscv64], 0.9.0-2+b2 [loong64], 0.9.0-2+b1 [amd64, armhf, i386, 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 (1.0.0-2)

rapid ribosomal RNA prediction

bart (1.0.00-2)

tools for computational magnetic resonance imaging

bart-view (0.3.00-1+b3 [arm64], 0.3.00-1+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

viewer for multi-dimensional complex-valued data

bbmap (39.20+dfsg-3)

BBTools genomic aligner and other tools for short sequences

bbmap-jni (39.20+dfsg-3+b2 [loong64], 39.20+dfsg-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

short read aligner and other bioinformatic tools - JNI library

bcalm (2.2.3-6+b1 [arm64, loong64], 2.2.3-6 [amd64, ppc64el, riscv64])

de Bruijn compaction in low memory

bcftools (1.22-1+b1 [arm64, loong64], 1.22-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

genomic variant calling and manipulation of VCF/BCF files

beads (1.1.22+ds-1+b1 [arm64], 1.1.22+ds-1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

2-DE electrophoresis gel image spot detection

beagle (250227-2)

Genotype calling, genotype phasing and imputation of ungenotyped markers

bedops (2.4.42+dfsg-1+b1 [arm64, loong64], 2.4.42+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

high-performance genomic feature operations

bedtools (2.31.1+dfsg-3+b1 [loong64], 2.31.1+dfsg-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

suite of utilities for comparing genomic features

bedtools-test (2.31.1+dfsg-3)

test data for the bedtools package

berkeley-express (1.5.3+dfsg-7+b1)

Streaming quantification for high-throughput sequencing

bio-eagle (2.4.1-3+b4)

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+b3 [arm64, riscv64], 2.0.4+dfsg-2+b1 [loong64], 2.0.4+dfsg-2 [amd64, armhf, i386, ppc64el, s390x])

clustering and assembling short reads for bioinformatics

bio-vcf (0.9.5-4)

domain specific language (DSL) for processing the VCF format

bioawk (1.0-5+b2 [arm64], 1.0-5+b1 [loong64], 1.0-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

extension of awk for biological sequence analysis

biobambam2 (2.0.185+ds-2+b1 [loong64], 2.0.185+ds-2 [amd64, ppc64el, riscv64])

tools for early stage alignment file processing

biogenesis (0.8-3.3)

artificial life program that simulates evolution of organisms

bioperl (1.7.8-3)

Perl tools for computational molecular biology

biosig-tools (3.9.5-1)

format conversion tools for biomedical data formats

biosquid (1.9g+cvs20050121-16+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+dfsg2-1+b1 [arm64, loong64], 0.7.5+dfsg2-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Bayesian Inference of Transcripts from Sequencing Data

bitwise (0.50-1+b3 [arm64], 0.50-1+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Interactive bitwise operation in ncurses

bitwuzla (0.8.2-2)

SMT solver for bit vectors and arrays

bitwuzla-dev (0.8.2-2)

SMT solver for bit vectors and arrays (development files)

bkchem (0.14.0~pre4+git20211228-5)

Chemical structures editor

blasr (5.3.5+dfsg-8+b1 [arm64, loong64], 5.3.5+dfsg-8 [amd64, ppc64el, riscv64])

mapping single-molecule sequencing reads

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

BlueBrain HPC Team C++ Development Guidelines

bmt (0.6-2)

software analysis benchmarking toolkit

bodr (10-3)

Blue Obelisk Data Repository

bolt-lmm (2.4.1+dfsg-2+b1)

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

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

Examples for bolt-lmm

boolector (3.2.4-1+b1 [loong64], 3.2.4-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

SMT solver for bit-vectors and arrays

bornagain (23.0-7)

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

bowtie (1.3.1-3+b3 [arm64], 1.3.1-3 [amd64, loong64, 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 (2.5.5-1+b1 [amd64, arm64, ppc64el, riscv64], 2.5.5-1 [loong64])

ultrafast memory-efficient short read aligner

bowtie2-examples (2.5.5-1)

Examples for bowtie2

boxshade (3.3.1-14+b2 [arm64, riscv64], 3.3.1-14+b1 [loong64], 3.3.1-14 [amd64, armhf, i386, ppc64el, s390x])

Pretty-printing of multiple sequence alignments

bppphyview (0.6.1-6+b1 [arm64, loong64], 0.6.1-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Bio++ Phylogenetic Viewer

bppsuite (2.4.1-8+b1 [arm64, loong64], 2.4.1-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Bio++ program suite

bppsuite-examples (2.4.1-8)

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+b1 [loong64], 0.95+dfsg-3 [amd64, arm64, armhf, i386, ppc64el, s390x])

BLAST Ring Image Generator

btllib-tools (1.7.5+dfsg-2+b1 [arm64, loong64], 1.7.5+dfsg-2 [amd64, ppc64el, riscv64, s390x])

Bioinformatics Technology Lab common code library tools

btor2tools (1.0.2~git20250918.d33c73f-1)

generic parser and tools for the BTOR2 format

busco (6.0.0-1)

benchmarking sets of universal single-copy orthologs

bustools (0.45.1+dfsg-2)

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

bwa (0.7.19-1+b1 [arm64, loong64], 0.7.19-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Burrows-Wheeler Aligner

bwa-mem2 (2.3+ds-1)

Sequence alignment using Burrows-Wheeler Transform

c-munipack (2.1.39-3)

reduction of images carried out by CCD camera

c-munipack-share (2.1.39-3)

reduction of images carried out by CCD camera (share)

c2x (2.42.a+ds-2+b1 [arm64, loong64], 2.42.a+ds-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

converter between DFT electronic structure codes formats

calceph (4.0.5-4)

Planetary ephemeris data access tools

calculix-ccx (2.21-1+b2 [arm64], 2.21-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Three-Dimensional Structural Finite Element Program

calculix-cgx (2.21+dfsg-2+b1 [arm64, loong64], 2.21+dfsg-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

callisto (1.1.0-3+b2 [arm64], 1.1.0-3+b1 [loong64], 1.1.0-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Daemon for e-Callisto hardware

camitk-actionstatemachine (6.0.0-3)

pipeline replay application for the CamiTK library

camitk-config (6.0.0-3)

Computer Assisted Medical Intervention Tool Kit - config

camitk-imp (6.0.0-3)

workbench application for the CamiTK library

casacore-data-igrf (12-3)

International Geomagnetic Reference Field data for casacore

casacore-data-jpl-de200 (2007.07.05+ds.1-2)

Jet Propulsion Laboratory Development Ephemeris DE200 for casacore

casacore-data-jpl-de405 (2007.07.05+ds.1-2)

Jet Propulsion Laboratory Development Ephemeris DE405 for casacore

casacore-data-lines (0+git2016.11.26-3)

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 (2-7)

Table of ICRF reference source coordinates for casacore

casacore-data-tai-utc (1.3)

Difference table between TAI and UTC for casacore

casacore-tools (3.8.0-5)

Tools built with CASA

casadi (3.7.0+ds2-3)

Nonlinear optimization and algorithmic differentiation

cassbeam (1.1-5+b1 [arm64], 1.1-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Cassegrain antenna modelling

cassiopee (1.0.9-5+b1)

index and search tool in genomic sequences

cat-bat (6.0.1-1+b1 [loong64], 6.0.1-1 [amd64, arm64, ppc64el, riscv64, s390x])

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

catfishq (1.4.0+ds-1)

concatenates fastq files

cba (0.3.6-6+b4 [amd64, arm64, armhf, i386, ppc64el, s390x], 0.3.6-6+b3 [riscv64], 0.3.6-6+b1 [loong64])

Continuous Beam Analysis

cbflib-bin (0.9.7+dfsg1-5.1+b1)

utilities to manipulate CBF files

cclib (1.8.1-3)

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+b2 [arm64], 4.8.1-4+b1 [loong64, riscv64], 4.8.1-4 [amd64, armhf, i386, ppc64el, s390x])

suite of programs designed to quickly group sequences

cdbfasta (1.00+git20230710.da8f5ba+dfsg-1+b3 [arm64], 1.00+git20230710.da8f5ba+dfsg-1+b2 [riscv64], 1.00+git20230710.da8f5ba+dfsg-1+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

Constant DataBase indexing and retrieval tools for multi-FASTA files

centrifuge (1.0.4.2-1+b1 [arm64, loong64], 1.0.4.2-1 [amd64, ppc64el, riscv64])

rapid and memory-efficient system for classification of DNA sequences

cg3 (1.5.1-2)

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

cg3-dev (1.5.1-2)

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

cgns-convert (4.5.0-1+b1)

CFD General Notation System - Conversion tools

cgview (0.0.20100111-8)

Circular Genome Viewer

ch5m3d (1.2.5+dfsg-3)

create and visualize 3-dimensional drawings of simple molecules

changeo (1.3.0-4)

Repertoire clonal assignment toolkit (Python 3)

checkit-tiff (1.7.3-1)

conformance checker for baseline TIFFs

chemical-structures (2.2.dfsg.1-1)

web service providing molecular structures in open formats

chemical-structures-data (2.2.dfsg.1-1)

set of molecular structures in open formats

chemonomatopist (0.11.5-1)

derive IUPAC systematic names for chemical structures

chimeraslayer (20101212+dfsg1-6)

detects likely chimeras in PCR amplified DNA

chip-seq (1.5.5-3+b3 [arm64], 1.5.5-3+b2 [riscv64], 1.5.5-3+b1 [loong64], 1.5.5-3 [amd64, armhf, i386, 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 (1.27+dfsg-1)

Chromatin state discovery and characterization

chromimpute (1.0.3+dfsg-6)

Large-scale systematic epigenome imputation

cif-linguist (0.4.2-6+b3)

transform CIF data among CIF formats and dialects

cif-tools (2.0.0-1)

Suite of tools to manipulate, validate and query mmCIF files

cif2hkl (1.4.7+ds1-2)

Convert crystallographic descriptions into HKL F^2 reflection lists

circos (0.69.9+dfsg-3)

plotter for visualizing data

circos-tools (0.23-1)

plotter for visualizing data - helper utilities

ckon (0.7.1-6)

automatic build tool for ROOT data analysis software

clearcut (1.0.9+git20211013.b799afe-1+b2 [arm64], 1.0.9+git20211013.b799afe-1+b1 [loong64, riscv64], 1.0.9+git20211013.b799afe-1 [amd64, armhf, i386, ppc64el, s390x])

extremely efficient phylogenetic tree reconstruction

clonalframe (1.2-11+b4 [arm64], 1.2-11+b3 [amd64, armhf, i386, ppc64el, s390x], 1.2-11+b2 [riscv64], 1.2-11+b1 [loong64])

inference of bacterial microevolution using multilocus sequence data

clonalframeml (1.13-2)

Efficient Inference of Recombination in Whole Bacterial Genomes

clonalorigin (1.0-9+b1 [loong64], 1.0-9 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

inference of homologous recombination in bacteria using whole genome sequences

clustalo (1.2.4-8+b2 [arm64], 1.2.4-8+b1 [loong64], 1.2.4-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

General-purpose multiple sequence alignment program for proteins

clustalw (2.1+lgpl-7+b3 [arm64], 2.1+lgpl-7+b2 [armhf, i386, riscv64], 2.1+lgpl-7+b1 [loong64], 2.1+lgpl-7 [amd64, ppc64el, s390x])

global multiple nucleotide or peptide sequence alignment

clustalx (2.1+lgpl-9+b3 [arm64], 2.1+lgpl-9+b2 [loong64, riscv64], 2.1+lgpl-9+b1 [amd64, armhf, i386, ppc64el, s390x])

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

cmor-tables (3.3-2)

MIP tables for the Climate Model Output Rewriter library

cmtk (3.3.1p2+dfsg-4+b1)

Computational Morphometry Toolkit

cnrun-tools (2.1.0-4+b1 [loong64], 2.1.0-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

NeuroML-capable neuronal network simulator (tools)

cod-tools (3.12.0+dfsg-1)

tools for manipulating CIF format files

codonw (1.4.4-8+b2 [arm64], 1.4.4-8+b1 [loong64], 1.4.4-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Correspondence Analysis of Codon Usage

coinor-cbc (2.10.13+ds-1)

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

coinor-clp (1.17.10+ds-1+b2)

Coin-or linear programming solver

coinor-csdp (6.2.0-6+b2)

Software package for semidefinite programming (binaries)

coinor-ipopt (3.14.19-1+b2)

Interior-Point Optimizer for large-scale nonlinear optimization

coinor-libbonmin4t64 (1.8.9-3+b2)

COIN-OR mixed integer programming

coinor-libcbc3.1 (2.10.13+ds-1)

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

coinor-libcgl1 (0.60.9+ds-1+b2)

COIN-OR Cut Generation Library

coinor-libclp1 (1.17.10+ds-1+b2)

Coin-or linear programming solver (shared libraries)

coinor-libcoinutils3v5 (2.11.12+ds-1+b2)

COIN-OR collection of utility classes (shared libraries)

coinor-libosi1v5 (0.108.11+ds-1+b2)

COIN-OR Open Solver Interface

coinor-libsymphony3 (5.7.2+dfsg-1+b2)

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

coinor-libvol1 (1.5.4-5+b1)

Coin-or linear programming solver (libraries)

coinor-symphony (5.7.2+dfsg-1+b2)

COIN-OR solver for mixed-integer linear programs

comet-ms (2019015+cleaned1-4.1+b2 [arm64], 2019015+cleaned1-4.1+b1 [loong64], 2019015+cleaned1-4.1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Tandem mass spectrometry (MS/MS) search engine

concavity (0.1+dfsg.1-6+b1 [arm64, loong64], 0.1+dfsg.1-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

predictor of protein ligand binding sites from structure and conservation

conda-package-handling (2.4.0-1)

create and extract conda packages of various formats

condor (25.10.1+dfsg-2)

distributed workload management system

condor-annex-ec2 (25.10.1+dfsg-2)

distributed workload management system - single node configuration

condor-kbdd (25.10.1+dfsg-2)

distributed workload management system - single node configuration

condor-test (25.10.1+dfsg-2)

distributed workload management system - single node configuration

condor-vm-gahp (25.10.1+dfsg-2)

distributed workload management system - single node configuration

conducteo (5.0.2-1)

thermal bridge simulation software (EN 10211)

connectome-workbench (2.1.0+dfsg-2+b1)

brain visualization, analysis and discovery tool

conservation-code (20110309.0-8)

protein sequence conservation scoring tool

coot (1.1.18+dfsg-5)

model building program for macromolecular crystallography

coot-data (1.1.18+dfsg-5)

various data files needed by Coot

coot-doc (1.1.18+dfsg-5)

documentation for Coot

covtobed (1.3.5+dfsg-2+b3 [arm64], 1.3.5+dfsg-2+b2 [riscv64], 1.3.5+dfsg-2+b1 [amd64, armhf, i386, loong64, 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

cp2k (2025.2-3)

Ab Initio Molecular Dynamics

cp2k-data (2025.2-3)

Ab Initio Molecular Dynamics (data files)

cpptraj (5.1.0+dfsg-5)

fast, parallelized molecular dynamics trajectory data analysis

cpuinfo (0.0~git20250905.877328f-1+b1)

CPU INFOrmation library (binary utilities)

crac (2.5.2+dfsg-7+b1 [arm64, loong64], 2.5.2+dfsg-7 [amd64, ppc64el, riscv64])

integrated RNA-Seq read analysis

critterding (1.0-beta12.1+dfsg-1+b1 [arm64, loong64], 1.0-beta12.1+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Evolving Artificial Life

ctdconverter (3.0a1-1)

Convert CTD files into Galaxy tool and CWL CommandLineTool files

ctffind (4.1.14-3+b2 [arm64], 4.1.14-3+b1 [loong64], 4.1.14-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast and accurate defocus estimation from electron micrographs

ctsim (6.0.2-7+b1 [arm64, loong64], 6.0.2-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Computed tomography simulator

ctsim-help (6.0.2-7)

Online help file for CTSim

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 (1.2.15+ds-1)

Common Workflow Language standalone document upgrader

cwlformat (2022.02.18-5)

code formatter for Common Workflow Language

cwltest (2.6.20251216093331-1)

Common Workflow Language testing framework

cwltool (3.2.20260413085819-1)

Common Workflow Language reference implementation

cwltool-doc (3.2.20260413085819-1)

Common Workflow Language reference implementation -- docs

daligner (1.0+git20240119.335105d-3+b2 [arm64], 1.0+git20240119.335105d-3+b1 [loong64], 1.0+git20240119.335105d-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

local alignment discovery between long nucleotide sequencing reads

damapper (0.0+git20240314.b025cf9-1+b1 [arm64, loong64], 0.0+git20240314.b025cf9-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

long read to reference genome mapping tool

darknet (0.0.0+git20180914.61c9d02e-3+b2 [riscv64], 0.0.0+git20180914.61c9d02e-3+b1 [amd64, arm64, armhf, i386, ppc64el, s390x], 0.0.0+git20180914.61c9d02e-3 [loong64])

Open Source Neural Networks in C

dascrubber (1.1-4+b2 [arm64], 1.1-4+b1 [loong64, riscv64], 1.1-4 [amd64, armhf, i386, ppc64el, s390x])

alignment-based scrubbing pipeline for DNA sequencing reads

datalad (1.3.1-2)

data files management and distribution platform

datalad-container (1.2.6-3)

DataLad extension for working with containerized environments

dawg (1.2-5+b1 [arm64, loong64], 1.2-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

simulate the evolution of recombinant DNA sequences

dazzdb (1.0+git20250217.a3eefd4-1+b1 [arm64, loong64], 1.0+git20250217.a3eefd4-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

manage nucleotide sequencing read data

dcl-f77 (7.5.3-1)

GFD-DENNOU Club Library (DCL) - FORTRAN77 version

dcm2niix (1.0.20250506-2)

next generation DICOM to NIfTI converter

dcmtk (3.7.0+really3.7.0-5)

OFFIS DICOM toolkit command line utilities

dcmtk-data (3.7.0+really3.7.0-5)

OFFIS DICOM toolkit data files

debian-astro-logo (5.0)

Debian Astronomy Pure Blends Logo

delly (1.7.2-2+b1)

Structural variant discovery by read analysis

density-fitness (1.2.1-1)

Calculates per-residue electron density scores

dextractor (1.0-7+b1 [arm64, loong64], 1.0-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

(d)extractor and compression command library

dh-r (20250812)

Debian helper tools for packaging R libraries

dialign (2.2.1-13+b2 [arm64], 2.2.1-13+b1 [loong64], 2.2.1-13 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Segment-based multiple sequence alignment

dialign-tx (1.0.2-15+b2 [arm64], 1.0.2-15+b1 [loong64], 1.0.2-15 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Segment-based multiple sequence alignment

dialign-tx-data (1.0.2-15)

Segment-based multiple sequence alignment (data files)

diamond-aligner (2.1.14-1+b1 [arm64, loong64], 2.1.14-1 [amd64, ppc64el, riscv64, s390x])

accelerated BLAST compatible local sequence aligner

dimbl (0.17-3+b2 [arm64], 0.17-3+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Distributed Memory Based Learner

discosnp (1:2.6.2-5+b1 [arm64, loong64], 1:2.6.2-5 [amd64, ppc64el, riscv64])

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

disulfinder (1.2.11-13+b1 [arm64, loong64], 1.2.11-13 [amd64, armhf, i386, ppc64el, riscv64, s390x])

cysteines disulfide bonding state and connectivity predictor

disulfinder-data (1.2.11-13)

data files for predictor of disulfide bonds in proteins

dlmodelbox (1.1.1-1)

Swiss Army Knife of Deep Learning Models

dnaclust (3-8+b2 [arm64], 3-8+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

tool for clustering millions of short DNA sequences

dnapi (1.1-3)

adapter prediction for small RNA sequencing - utils

dnarrange (1.6.3-3)

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

doris (5.0.3~beta+dfsg-19) [contrib]

Delft object-oriented radar interferometric software

dozzaqueux (3.51-5)

simulator for chemical mixtures

dozzaqueux-data (3.51-5)

databases for chemical mixtures

dpuser (4.3+dfsg-1+b1 [arm64, loong64], 4.3+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Interactive language for handling numbers, strings, and matrices

drat-trim (0.0~git20240428.effa1dc-3)

DART-trim satisfiability proof checker (binary utils)

drat-trim-examples (0.0~git20240428.effa1dc-3)

DART-trim satisfiability proof checker (example files)

drawxtl (5.5-6.1+b3 [arm64], 5.5-6.1+b2 [armhf, riscv64], 5.5-6.1+b1 [amd64, i386, loong64, ppc64el, s390x])

crystal structure viewer

drop-seq-testdata (3.0.2+dfsg-2)

analyzing Drop-seq data (testdata)

drop-seq-tools (3.0.2+dfsg-2)

analyzing Drop-seq data

drs4eb (5.0.6+git20211217+ds-5+b1 [arm64, loong64], 5.0.6+git20211217+ds-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

DRS4 Evaluation Board software

drslib (0.3.2-3)

Command-line tools for the Data Reference Syntax library

dsdp (5.8-12+b1 [arm64, loong64], 5.8-12 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Software for Semidefinite Programming

dssp (4.6.1-1)

protein secondary structure assignment based on 3D structure

dualword-rt (0.4.0-1+b1 [arm64, loong64], 0.4.0-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

program for measuring bimanual simple visual reaction time

dwgsim (0.1.14-4+b1 [arm64, loong64], 0.1.14-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

short sequencing read simulator

dx (1:4.4.4-19+b1 [arm64, loong64], 1:4.4.4-19 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

dyssol (1.5.0-1.1)

Tool for dynamic flowsheet simulation - command line tool

dyssol-data (1.5.0-1.1)

Tool for dynamic flowsheet simulation - data files

dyssol-gui (1.5.0-1.1)

Tool for dynamic flowsheet simulation - GUI

e-mem (1.0.1-5+b3 [arm64], 1.0.1-5+b2 [loong64, riscv64], 1.0.1-5 [amd64, armhf, i386, ppc64el, s390x])

Efficient computation of Maximal Exact Matches for very large genomes

e00compr (1.0.1-8+b1 [arm64, loong64], 1.0.1-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Program to read/write Arcinfo compressed E00 files

ecaccess (6.3.1-1)

clients to access ECMWF facilities

ecflow-client (5.16.0-1)

Client tools for Meteorological workflow

ecflow-server (5.16.0-1)

Meteorological workflow controller - server

ecopcr (1.0.1+dfsg-6)

estimate PCR barcode primers quality

ectrans-utils (1.8.0-1)

Spherical Harmonics Transforms library - utilities

edfbrowser (2.14+dfsg-1+b2 [loong64], 2.14+dfsg-1+b1 [arm64], 2.14+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64])

viewer for biosignal storage files such as bdf and edf

edlib-aligner (1.2.7-7+b1)

edlib sequence alignment tool using edit distance

edtsurf (0.2009-10+b2 [arm64], 0.2009-10+b1 [loong64, riscv64], 0.2009-10 [amd64, armhf, i386, ppc64el, s390x])

triangulated mesh surfaces for protein structures

edu-sync (0.3.2+ds-6)

Moodle synchronization utility

eigensoft (8.0.0+dfsg-2+b2 [arm64], 8.0.0+dfsg-2+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

reduction of population bias for genetic analyses

elastix (5.3.1-1)

toolbox for rigid and nonrigid registration of images

elk-lapw (10.4.9-1+b1 [arm64], 10.4.9-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

All-Electron Density-Functional Electronic Structure Code

elph (1.0.1-5+b2 [arm64], 1.0.1-5+b1 [loong64, riscv64], 1.0.1-5 [amd64, armhf, i386, ppc64el, s390x])

DNA/protein sequence motif finder

embassy-domainatrix (0.1.660-5+b2 [arm64], 0.1.660-5+b1 [loong64], 0.1.660-5 [amd64, ppc64el, riscv64])

Extra EMBOSS commands to handle domain classification file

embassy-domalign (0.1.660-5+b2 [arm64], 0.1.660-5+b1 [loong64], 0.1.660-5 [amd64, ppc64el, riscv64])

Extra EMBOSS commands for protein domain alignment

embassy-domsearch (1:0.1.660-4+b2 [arm64], 1:0.1.660-4+b1 [loong64], 1:0.1.660-4 [amd64, ppc64el, riscv64])

Extra EMBOSS commands to search for protein domains

emboss (6.6.0+dfsg-18+b1 [loong64], 6.6.0+dfsg-18 [amd64, arm64, ppc64el, riscv64, s390x])

European molecular biology open software suite

emboss-data (6.6.0+dfsg-18)

data files for the EMBOSS package

emboss-explorer (2.2.0-12)

web-based GUI to EMBOSS

emboss-lib (6.6.0+dfsg-18+b1 [loong64], 6.6.0+dfsg-18 [amd64, arm64, ppc64el, riscv64, s390x])

EMBOSS Libraries

emmax (0~beta.20100307-6+b1 [arm64, loong64], 0~beta.20100307-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

genetic mapping considering population structure

engauge-digitizer (12.9.1+ds-2)

interactively extracts numbers from bitmap graphs or maps

ent (1.2debian-3+b2 [arm64, loong64], 1.2debian-3+b1 [riscv64], 1.2debian-3 [amd64, armhf, i386, ppc64el, s390x])

pseudorandom number sequence test program

epics-base (7.0.8.1+dfsg1-10)

EPICS tools

ergo (3.8.2-1.1+b1 [arm64, loong64], 3.8.2-1.1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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 (25.05pl1.1-2+b1 [loong64], 25.05pl1.1-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

European Southern Observatory Munich Image Data Analysis System

eso-midas-testdata (25.05pl1.1-2)

Test data files for ESO-MIDAS

esorex (3.13.7+ds-2+b1 [arm64, loong64], 3.13.7+ds-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Execution Tool for European Southern Observatory pipelines

estscan (3.0.3-6+b2 [arm64], 3.0.3-6+b1 [loong64, riscv64], 3.0.3-6 [amd64, armhf, i386, ppc64el, s390x])

ORF-independent detector of coding DNA sequences

esys-particle (2.3.5+dfsg2-13)

Software for particle-based numerical modelling (MPI version)

etsf-io (1.0.4-6+b1 [arm64, loong64], 1.0.4-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Binary tools to check, merge and read ETSF files

examl (3.0.22-7+b2 [arm64], 3.0.22-7+b1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference

exonerate (2.4.0-5+b3 [arm64], 2.4.0-5+b2 [riscv64], 2.4.0-5+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

generic tool for pairwise sequence comparison

expeyes (5.3.5+repack-1)

hardware & software framework for developing science experiments

expeyes-clib (5.3.5+repack-1)

hardware & software framework for developing science experiments

eye (1:11.24.4+ds-1)

semantic web reasoning engine

eyes17 (5.3.5+repack-1)

hardware & software framework for developing science experiments

eyes17-manuals-en (5.3.4+repack-1)

Eyes17 User Manuals (English version)

eyes17-manuals-es (5.3.4+repack-1)

Eyes17 User Manuals (Spanish version)

eyes17-manuals-fr (5.3.4+repack-1)

Eyes17 User Manuals (French version)

eyes17-manuals-ml (5.3.4+repack-1)

Eyes17 User Manuals (Malayalam version)

fast5 (0.6.5-9)

utilities for manipulating Oxford Nanopore Fast5 files

fasta3 (36.3.8i.14-Nov-2020-4+b1 [arm64, loong64], 36.3.8i.14-Nov-2020-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

tools for searching collections of biological sequences

fastahack (1.0.0+dfsg-11+b3)

utility for indexing and sequence extraction from FASTA files

fastani (1.34+ds-1+b1 [arm64, loong64], 1.34+ds-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

fastaq (3.17.0-9)

FASTA and FASTQ file manipulation tools

fastdnaml (1.2.2-18+b2 [loong64], 1.2.2-18+b1 [arm64], 1.2.2-18 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Tool for construction of phylogenetic trees of DNA sequences

fastlink (4.1P-fix100+dfsg-6+b1 [arm64, loong64], 4.1P-fix100+dfsg-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

faster version of pedigree programs of Linkage

fastml (3.11-5)

maximum likelihood ancestral amino-acid sequence reconstruction

fastp (1.0.1+dfsg-1+b1 [arm64, loong64], 1.0.1+dfsg-1 [amd64, ppc64el, riscv64, s390x])

Ultra-fast all-in-one FASTQ preprocessor

fastq-pair (1.0-5+b1 [arm64, loong64], 1.0-5 [amd64, armhf, i386, ppc64el, riscv64, 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-5+b2 [arm64], 2.184+v7+dfsg-5+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

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

fasttext (0.9.2+ds-9+b1)

Efficient learning of word representations and sentence classification library

fasttree (2.1.11-2+b2 [arm64], 2.1.11-2+b1 [loong64, riscv64], 2.1.11-2 [amd64, armhf, i386, ppc64el, s390x])

phylogenetic trees from alignments of nucleotide or protein sequences

fcc (2.16-2+b1)

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

feedgnuplot (1.64-1)

Pipe-oriented frontend to Gnuplot

feenox (1.2-1+b3 [arm64], 1.2-1+b2 [amd64, ppc64el, riscv64, s390x])

cloud-first free no-X uniX-like finite-element(ish) tool

feff85exafs (0.2+dfsg-3+b1 [loong64], 0.2+dfsg-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Open Source theoretical EXAFS calculations

ffindex (0.9.9.9-7+b2 [arm64], 0.9.9.9-7+b1 [amd64, ppc64el, riscv64, s390x], 0.9.9.9-7 [armhf, i386])

simple index/database for huge amounts of small files

fiat-utils (2.0.0-1)

Fortran IFS and Arpege Toolkit - utilities

figtree (1.4.4-7)

graphical phylogenetic tree viewer

filtlong (0.3.1-1)

quality filtering tool for long reads of genome sequences

filtlong-data (0.3.1-1)

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

firm-phoenix-ware (4.7.5+repack-3)

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+b2 [arm64], 1.4.4-6+b1 [loong64], 1.4.4-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Extract cutouts from FITS image format files

fitsh (0.9.4-2+b2 [loong64], 0.9.4-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Software package for astronomical image processing

fitspng (2.0-2+b3 [arm64], 2.0-2+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

FITS to PNG converter

fitsverify (4.22+cfitsio4.6.4-1)

transitional dummy package

fitsverify

virtual package provided by libcfitsio-bin

fityk (1.3.2-3+b6 [arm64], 1.3.2-3+b5 [armhf, riscv64], 1.3.2-3+b4 [amd64, i386, ppc64el, s390x], 1.3.2-3+b1 [loong64])

general-purpose nonlinear curve fitting and data analysis

flash (1.2.11-2+b2 [arm64], 1.2.11-2+b1 [loong64, riscv64], 1.2.11-2 [amd64, armhf, i386, ppc64el, s390x])

Fast Length Adjustment of SHort reads

flexbar (1:3.5.0-8)

flexible barcode and adapter removal for sequencing platforms

flextra (5.0-19)

Trajectory model for tracing air transport phenomena

flye (2.9.6+dfsg-2+b1 [arm64, loong64], 2.9.6+dfsg-2 [amd64, ppc64el, riscv64, s390x])

de novo assembler for single molecule sequencing reads using repeat graphs

fml-asm (0.1+git20221215.85f159e-1+b2)

tool for assembling Illumina short reads in small regions

folialint (2.21.1-2)

Implementation of the FoLiA document format (C++ headers)

foma (1:0.10.0+s311.20250909-2)

Tools for constructing various finite-state automata

form (5.0.0-2+b1)

Symbolic manipulation system

fractalnow (0.8.2-5+b4 [arm64], 0.8.2-5+b3 [riscv64], 0.8.2-5+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

Fast, advanced fractal generator

free42-nologo (3.3.12+ds-1)

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

freecad (1.1.1+dfsg-2)

Extensible Open Source CAx program

freecad-common (1.1.1+dfsg-2)

Extensible Open Source CAx program - common files

freecad-python3 (1.1.1+dfsg-2)

Extensible Open Source CAx program - Python 3 binaries

freecontact (1.0.21-16+b1)

fast protein contact predictor

freesasa (2.1.2-6+b1 [loong64], 2.1.2-6 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Solvent Accessible Surface Area of biomolecules

frog (0.34-2)

tagger and parser for natural languages (runtime)

frogdata (0.22-2)

Data files for Frog

fsa (1.15.9+dfsg-6+b3 [arm64], 1.15.9+dfsg-6+b2 [riscv64], 1.15.9+dfsg-6+b1 [loong64], 1.15.9+dfsg-6 [amd64, armhf, i386, ppc64el, s390x])

Fast Statistical Alignment of protein, RNA or DNA sequences

fsm-lite (1.0-8+b2 [arm64], 1.0-8+b1 [loong64, riscv64], 1.0-8 [amd64, 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+b2)

Curve plotting and image display interface tool

funtools (1.4.8-2+b2)

Minimal buy-in FITS utility package

fxt-tools (0.3.15-1+b2)

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 (0.40-1)

reads data from a device with graphical plots and evaluation

garli (2.1-9+b1 [arm64], 2.1-9 [amd64, armhf, i386, ppc64el, riscv64, s390x])

phylogenetic analysis of molecular sequence data using maximum-likelihood

garli-examples (2.1-9)

phylogenetic analysis of molecular sequence data (examples)

garli-mpi (2.1-9+b1 [arm64], 2.1-9 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

garlic (1.6-3+b2 [arm64], 1.6-3+b1 [amd64, loong64, riscv64], 1.6-3 [armhf, i386, 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+b5)

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 (3.0.2-3)

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

gbutils (6.3-1+b2 [arm64, loong64, riscv64], 6.3-1+b1 [amd64, armhf, i386, ppc64el, s390x])

utilities for command line econometrics

gdal-bin (3.13.1+dfsg-1)

Geospatial Data Abstraction Library - Utility programs

gdal-data (3.13.1+dfsg-1)

Geospatial Data Abstraction Library - Data files

gdal-plugins (3.13.1+dfsg-1)

Geospatial Data Abstraction Library - Plugins

gdl-astrolib (2022.09.12+dfsg-3)

Low-level astronomy software for GDL

gdl-coyote (2022.04.12-3)

GDL library from D. Fannings IDL courses

gdl-mpfit (1.85+2017.01.03-4)

Robust non-linear least squares curve fitting for GDL

gdpc (2.2.5-19)

visualiser of molecular dynamic simulations

gdpc-examples (2.2.5-19)

example files for the gdpc program

gemmi (0.7.5+ds-1)

library for structural biology - executable

genometester (4.0+git20221122.71e6625-1+b1 [loong64], 4.0+git20221122.71e6625-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

toolkit for performing set operations on k-mer lists

genomethreader (1.7.3+dfsg-12)

software tool to compute gene structure predictions

genometools (1.6.6+ds-2+b1 [arm64, loong64], 1.6.6+ds-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

versatile genome analysis toolkit

genometools-common (1.6.6+ds-2)

shared data files for GenomeTools

genomicsdb-tools (1.5.5-2)

sparse array storage library for genomics (tools)

gentle (1.9.5~alpha2+dfsg1-3+b1 [arm64, loong64], 1.9.5~alpha2+dfsg1-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

suite for molecular cloning and sequence analysis

geographiclib-tools (2.7-1+b1)

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

geotiff-bin (1.7.4-2)

GeoTIFF (geografic enabled TIFF) library -- tools

gerris (20131206+dfsg-22+b1)

Fluid Flow Solver

getdata (0.2-4)

management of external databases

gff2aplot (2.0-15+b3 [arm64], 2.0-15+b1 [loong64], 2.0-15 [amd64, armhf, i386, 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+b2 [arm64], 0.12.7-8+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

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

gftl-dev (1.3.0+is-really-1.2.7-2)

Containers and iterators for Fortran

gftl-shared-dev (1.0.7-3+b1 [loong64], 1.0.7-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Common gFTL containers of Fortran intrinsic types

ggd-utils (1.0.0+ds-3+b2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x], 1.0.0+ds-3+b1 [loong64])

programs for use in ggd

ghkl (5.1.9-1)

diffractometer computation control application

ghmm (0.9~rc3-12)

General Hidden-Markov-Model library - tools

ginga (6.0.0-1)

Astronomical image viewer

gjh-asl-json (0.0+git20210628.867c5da-1+b2 [arm64], 0.0+git20210628.867c5da-1+b1 [loong64, riscv64], 0.0+git20210628.867c5da-1 [amd64, ppc64el, s390x])

gjh solver, like solver from AMPL Library

glam2 (1064-10+b1 [arm64, loong64], 1064-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

gapped protein motifs from unaligned sequences

glgrib-data (1.0-6)

Display GRIB2 fields using OpenGL (data for glgrib)

glgrib-egl (1.0-6+b1)

Render geophysical fields encoded in GRIB edition 2 using OpenGL

glgrib-glfw (1.0-6+b1)

Interactive display for geophysical fields encoded in GRIB2

glgrib-shaders (1.0-6)

Display GRIB2 fields using OpenGL (shaders for glgrib)

glgrib-testdata (1.0-6)

Display GRIB2 fields using OpenGL (test data for glgrib)

glgrib-tk (1.0-6+b1)

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

glvis (4.5-1+b1)

accurate and flexible finite element visualization

gmap (2025-07-31+ds-1+b1 [arm64, loong64], 2025-07-31+ds-1 [amd64, armhf, i386, ppc64el, riscv64])

spliced and SNP-tolerant alignment for mRNA and short reads

gmt (6.6.0+dfsg-1+b3)

Generic Mapping Tools

gmt-common (6.6.0+dfsg-1)

Generic Mapping Tools - Architecture-independent files

gmt-dcw (2.2.0-1)

Digital Chart of the World (DCW) for GMT

gmt-gshhg (2.3.7-7)

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

gmt-gshhg-full (2.3.7-7)

Full resolution coastlines for the Generic Mapping Tools

gmt-gshhg-high (2.3.7-7)

High resolution coastlines for the Generic Mapping Tools

gmt-gshhg-low (2.3.7-7)

Low resolution coastlines for the Generic Mapping Tools

gmtsar (6.6+ds-1)

InSAR processing system based on Generic Mapping Tools - metapackage

gmtsar-core (6.6+ds-1+b2 [loong64], 6.6+ds-1+b1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

InSAR processing system based on Generic Mapping Tools - core

gmtsar-data (6.6+ds-1)

InSAR processing system based on Generic Mapping Tools - data

gmtsar-scripts (6.6+ds-1)

InSAR processing system based on Generic Mapping Tools - scripts

gnuastro (0.24-1+b1)

GNU Astronomy Utilities programs

goby-java (3.3.1+dfsg2-12)

next-generation sequencing data and results analysis tool

gpaw (25.7.0-2)

DFT and beyond within the projector-augmented wave method

gpaw-data (24.11.0-1)

gpaw datasets/setups

gpx (2.6.8-1+b2 [arm64], 2.6.8-1+b1 [loong64, riscv64], 2.6.8-1 [amd64, armhf, i386, ppc64el, s390x])

Gcode to x3g conversion post processor

grabix (0.1.7-6)

wee tool for random access into BGZF files

graphlan (1.1.3-6)

circular representations of taxonomic and phylogenetic trees

grass (8.5.0-1)

Geographic Resources Analysis Support System (GRASS GIS)

grass-core (8.5.0-1+b1)

GRASS GIS core components

grass-gui (8.5.0-1+b1)

GRASS GIS graphical user interfaces

gravit (0.5.1+dfsg-6+b3 [arm64], 0.5.1+dfsg-6+b2 [riscv64], 0.5.1+dfsg-6+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

visually stunning gravity simulator

gravit-data (0.5.1+dfsg-6)

data files for Gravit

gri (2.12.27-1.2+b1)

a language for scientific illustration

grinder (0.5.4-6)

Versatile omics shotgun and amplicon sequencing read simulator

gromacs (2026.2-2)

Molecular dynamics simulator, with building and analysis tools

gromacs-data (2026.2-2)

GROMACS molecular dynamics sim, data and documentation

groops (0+git20250907+ds-1) [non-free]

software toolkit for gravity field recovery and GNSS processing

groops-gui (0+git20250907+ds-1) [non-free]

software toolkit for gravity field recovery and GNSS processing (GUI)

gsort (0.1.5-1+b1 [loong64], 0.1.5-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

sort genomic data

gubbins (3.4.3-4)

phylogenetic analysis of genome sequences

gvb (1.4-1.2)

visual simulator of 1 and 2-dimensional vibrations

gwama (2.2.2+dfsg-6+b1 [arm64, loong64], 2.2.2+dfsg-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Genome-Wide Association Meta Analysis

gwyddion (3.10-6)

Scanning Probe Microscopy visualization and analysis tool

gwyddion-common (3.10-6)

architecture-independent files for Gwyddion SPM analysis tool

gyoto (2.0.2-8)

General relativistic geodesic integration and ray-tracing

gyoto-bin (2.0.2-8)

General relativistic ray-tracing command-line interface

h5utils (1.13.2-2+b1 [arm64, loong64], 1.13.2-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

HDF5 files visualization tools

harminv (1.4.2-2+b1 [loong64], 1.4.2-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

extraction of complex frequencies and amplitudes from time series

harvest-tools (1.3-8+b8 [arm64, armhf], 1.3-8+b6 [amd64, i386, ppc64el, s390x], 1.3-8+b5 [riscv64], 1.3-8+b1 [loong64])

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~git20221111.49e3b65-7+b1 [amd64, arm64, armhf, i386, loong64, ppc64el, s390x], 0.0~git20221111.49e3b65-7 [riscv64])

external filters for HDF5: LZ4, BZip2

hdf5-filter-plugin-blosc-serial (1.0.1-2+b1 [loong64], 1.0.1-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

blocking, shuffling and lossless compression library

hdf5-filter-plugin-zfp-serial (1.1.1-2+b4 [arm64], 1.1.1-2+b2 [amd64, armhf, i386, loong64, ppc64el, riscv64])

Compression plugin for the HDF5 library using ZFP compression

hdf5-helpers (1.14.6+repack-2+b1)

HDF5 - Helper tools

hdf5-tools (1.14.6+repack-2+b1)

HDF5 - Runtime tools

herisvm (0.9.0-2)

machine learning tools for classification algorithms

hfst (3.17.1-5)

Helsinki Finite-State Transducer Technology

hfst-ospell (0.5.4-2)

Spell checker library and tool based on HFST

hhsuite (3.3.0+ds-10+b1)

sensitive protein sequence searching based on HMM-HMM alignment

hhsuite-data (3.3.0+ds-10)

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

highs (1.14.0+ds-1)

High performance linear optimization software

hisat2 (2.2.1-5+b5 [arm64], 2.2.1-5+b4 [amd64], 2.2.1-5+b3 [armhf, i386, ppc64el, riscv64, s390x], 2.2.1-5 [loong64])

graph-based alignment of short nucleotide reads to many genomes

hmmer (3.4+dfsg-3+b1 [arm64], 3.4+dfsg-3 [amd64, i386])

profile hidden Markov models for protein sequence analysis

hmmer2 (2.3.2+dfsg-12+b3)

profile hidden Markov models for protein sequence analysis

hodie (1.5.0-5+b1 [loong64], 1.5.0-5 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

prints the date in Latin

horae (071~svn537+ds1-2) [contrib]

interactive graphical processing and analysis of EXAFS data

hpcc (1.5.0-4+b1)

HPC Challenge benchmark

hts-nim-tools (0.2.1-4+b1 [loong64], 0.2.1-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

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

hyphy-common (2.5.69+dfsg-2)

Hypothesis testing using Phylogenies (common files)

hyphy-mpi (2.5.69+dfsg-2+b1 [arm64], 2.5.69+dfsg-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Hypothesis testing using Phylogenies (MPI version)

hyphy-pt (2.5.69+dfsg-2+b1 [arm64], 2.5.69+dfsg-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Hypothesis testing using Phylogenies (pthreads version)

idba (1.1.3-8+b2 [arm64], 1.1.3-8+b1 [loong64, riscv64], 1.1.3-8 [amd64, armhf, i386, ppc64el, s390x])

iterative De Bruijn Graph short read assemblers

idba-extra (1.1.3-8+b2 [arm64], 1.1.3-8+b1 [loong64, riscv64], 1.1.3-8 [amd64, armhf, i386, ppc64el, s390x])

iterative De Bruijn Graph short read assemblers (extra tools)

idseq-bench (0.0~git20210602.27fb6dc-2)

Benchmark generator for the IDseq Portal

ifcopenshell (0.8.1+dfsg1-5)

Library for working with Industry Foundation Classes (IFC) data

ifeffit (2:1.2.11d-15+b1 [arm64, loong64], 2:1.2.11d-15 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Interactive XAFS analysis program

igblast (1.20.0-4)

Immunoglobulin and T cell receptor variable domain sequence analysis

igmplot (3.17-2)

identify, characterize, and quantify molecular interactions

igor (1.4.0+dfsg-5+b2 [arm64], 1.4.0+dfsg-5+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

infers V(D)J recombination processes from sequencing data

iitii (0.0+git20191030.85209e0-4+b1 [arm64, loong64], 0.0+git20191030.85209e0-4 [amd64, ppc64el, riscv64, s390x])

Implicit Interval Tree with Interpolation Index

illustrate (0.0+git20200923.217db48-2+b3 [arm64], 0.0+git20200923.217db48-2+b1 [amd64, armhf, i386, loong64, 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+b4 [arm64], 1.1.9h-4+b3 [amd64, armhf, i386], 1.1.9h-4+b2 [ppc64el, riscv64, s390x], 1.1.9h-4+b1 [loong64])

Image viewing and analysis application

indelible (1.03-7)

powerful and flexible simulator of biological evolution

indi-aagcloudwatcher-ng (1.7+20230106180155-2+b1 [arm64, loong64], 1.7+20230106180155-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for the AAG Cloud Watcher

indi-aok (2.0+20221222093242-2+b1 [arm64, loong64], 2.0+20221222093242-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for AOK Skywalker

indi-apogee (1.9+20221223184417-3+b1 [arm64, loong64], 1.9+20221223184417-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Apogee CCDs and Filter Wheels

indi-armadillo-platypus (1.0+20221226082641-3+b1 [arm64, loong64], 1.0+20221226082641-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Lunatico Astronomia Armadillo and Platypus

indi-asi (2.2+20221225102500-2) [contrib]

INDI Driver for ZWO Optics ASI cameras

indi-avalon (1.12+20221223132122-2+b1 [arm64, loong64], 1.12+20221223132122-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Avalon Instruments mounts

indi-beefocus (0.1+20221222010828-2+b1 [arm64, loong64], 0.1+20221222010828-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Bee Focus

indi-bresserexos2 (1.0+20221223130124-2+b1 [arm64, loong64], 1.0+20221223130124-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Exos II GoTo Telescope Mount

indi-dsi (0.4+20221223123028-3+b1 [arm64, loong64], 0.4+20221223123028-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Meade DSI Pro I/II/III

indi-eqmod (1.0+20230126190232-5)

INDI EQMod Driver

indi-ffmv (0.3+20221223120905-3+b1 [arm64, loong64], 0.3+20221223120905-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Point Grey Firefly MV cameras

indi-fishcamp (1.1-3) [contrib]

INDI driver for Fishcamp Engineering CCD

indi-fli (1.5+20221225141318-3+b1 [arm64, loong64], 1.5+20221225141318-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for FLI CCD & Focuser

indi-gige (0.1+20221223115700-3+b1 [arm64, loong64], 0.1+20221223115700-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for GigE machine vision cameras

indi-gphoto (3.2+20221221172841-3+b2 [arm64, loong64], 3.2+20221221172841-3+b1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for GPhoto (DSLR) Cameras

indi-gpsd (0.5+20221222000619-2+b3 [arm64], 0.5+20221222000619-2+b2 [amd64, armhf, i386, ppc64el, riscv64, s390x], 0.5+20221222000619-2+b1 [loong64])

INDI driver for gpsd GPS daemon

indi-gpsnmea (0.2+20221223114018-2+b1 [arm64, loong64], 0.2+20221223114018-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for GPS NMEA streams

indi-inovaplx (1.4+20221221105828-3) [contrib]

INDI driver for iNova PLX Cameras

indi-limesdr (1.4+20221223110308-2+b1 [arm64, loong64], 1.4+20221223110308-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for LimeSDR (LMS7) Receiver

indi-maxdomeii (1.3+20221223105522-3+b2 [loong64], 1.3+20221223105522-3+b1 [arm64], 1.3+20221223105522-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for MaxDome II dome control system

indi-mgen (0.1+20221222184336-2+b1 [arm64, loong64], 0.1+20221222184336-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Lacerta MGen Autoguider

indi-mi (1.8-2) [contrib]

INDI driver for cameras made by Moravian Instruments

indi-nexdome (1.5+20221222183051-2+b1 [arm64, loong64], 1.5+20221222183051-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for NexDome

indi-nightscape (1.0.6+20221222181314-4)

INDI driver for Celestron Nightscape 8300

indi-orion-ssg3 (0.1+20221222180647-3+b1 [arm64, loong64], 0.1+20221222180647-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI Driver for Orion StarShoot G3 and G4 cameras

indi-pentax (1.0+20221221102411-6) [contrib]

INDI driver for Pentax cameras

indi-playerone (0.9+20230105184731-4) [contrib]

INDI driver for cameras made by Playerone

indi-rtklib (1.0+20221222172722-2+b1 [arm64, loong64], 1.0+20221222172722-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for precise positioning with RTKLIB

indi-sbig (2.1+20221220234924-5) [contrib]

INDI driver for SBIG cameras

indi-shelyak (1.0+20221222171819-2+b2 [loong64], 1.0+20221222171819-2+b1 [arm64], 1.0+20221222171819-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Shelyak and Alpy Spectrograph

indi-starbook (0.8+20221222163625-2+b1 [arm64, loong64], 0.8+20221222163625-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Vixen Starbook telescope controllers

indi-starbook-ten (0.1-4+b1 [arm64, loong64], 0.1-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Vixen Starbook Ten telescope controllers

indi-sx (1.16+20221222162728-3+b1 [arm64, loong64], 1.16+20221222162728-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Starlight Xpress CCD and Filter Wheel

indi-talon6 (2.0+20221222160901-2+b1 [arm64, loong64], 2.0+20221222160901-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for Talon6 Roll Off Roof

indi-webcam (1.0+20221222161740-3+b1 [arm64, loong64], 1.0+20221222161740-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI Driver for web cameras

indi-weewx-json (1.0-3+b1 [arm64, loong64], 1.0-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

INDI driver for the WeeWX Weather Station

indigo-utils (1.4.3-1+b1 [loong64], 1.4.3-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Organic Chemistry Toolkit Utilities

infernal (1.1.5-3+b1 [arm64], 1.1.5-3 [amd64, i386])

inference of RNA secondary structural alignments

inhomog (0.1.9.2-1+b5 [arm64], 0.1.9.2-1+b4 [amd64, armhf, i386, ppc64el, s390x], 0.1.9.2-1+b2 [loong64, 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 (2.0.1-4)

sequencing simulator producing realistic Illumina reads

ipig (0.0.r5-5+b1 [loong64], 0.0.r5-5 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

integrating PSMs into genome browser visualisations

iqtree (2.4.0+dfsg-2)

efficient phylogenetic software by maximum likelihood

iqtree3 (3.1.1+dfsg-2)

efficient phylogenetic software by maximum likelihood; v3

iraf (2.18.1-2+b1 [arm64, loong64], 2.18.1-2 [amd64, armhf, i386, ppc64el, riscv64])

Image Reduction and Analysis Facility

iraf-dev (2.18.1-2+b1 [arm64, loong64], 2.18.1-2 [amd64, armhf, i386, ppc64el, riscv64])

Image Reduction and Analysis Facility (development files)

iraf-fitsutil (2024.07.06-2+b1 [loong64], 2024.07.06-2 [amd64, arm64, armhf, i386, ppc64el, riscv64])

FITS utilities for IRAF

iraf-mscred (5.05+2018.07.09-4+b1 [loong64], 5.05+2018.07.09-4 [amd64, arm64, armhf, i386, ppc64el, riscv64])

CCD mosaic reduction package for IRAF

iraf-noao (2.18.1-2+b1 [arm64, loong64], 2.18.1-2 [amd64, armhf, i386, ppc64el, riscv64])

IRAF NOAO data reduction package

iraf-noao-dev (2.18.1-2+b1 [arm64, loong64], 2.18.1-2 [amd64, armhf, i386, ppc64el, riscv64])

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 (1.2.1-1+b1 [loong64], 1.2.1-1 [amd64, arm64, armhf, i386, ppc64el, riscv64])

Selected tools from the Space Telescope Science Data Analysis System

iraf-wcstools (3.9.7-2)

Handle the WCS of a FITS image (IRAF package)

iraf-xdimsum (2003.01.24-3+b1 [loong64], 2003.01.24-3 [amd64, arm64, armhf, i386, ppc64el, riscv64])

Deep Infrared Mosaicing Software

irstlm (6.00.05-7+b2)

IRST Language Modeling Toolkit

ismrmrd-schema (1.15.0-3)

schema for ISMRMRD

ismrmrd-tools (1.15.0-3)

command-line tools for ISMRMRD

iso2mesh-demos (1.9.8+ds-3)

sample files and demo scripts for Iso2Mesh toolbox

iso2mesh-tools (1.9.8+ds-3)

3D mesh generation and repairing utilities

iva (1.0.11+ds-6+b1 [loong64], 1.0.11+ds-6 [amd64, arm64, armhf, i386, ppc64el, riscv64])

iterative virus sequence assembler

ivar (1.4.4+dfsg-2)

functions broadly useful for viral amplicon-based sequencing

jaligner (1.0+dfsg-11)

Smith-Waterman algorithm with Gotoh's improvement

jblas (1.2.5+dfsg-1+b1 [loong64, riscv64], 1.2.5+dfsg-1 [amd64, arm64, armhf, i386, ppc64el, s390x])

fast linear algebra library for Java

jellyfish (2.3.1-6)

count k-mers in DNA sequences

jellyfish-examples (2.3.1-6)

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

jellyfish1 (1.1.11-10+b2 [loong64], 1.1.11-10+b1 [arm64], 1.1.11-10 [amd64, ppc64el, riscv64])

count k-mers in DNA sequences

jemboss (6.6.0+dfsg-18)

graphical user interface to EMBOSS

jmodeltest (2.1.10+dfsg-14)

HPC selection of models of nucleotide substitution

jmol (16.3.55+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 (2.7.1-3)

JUBE Benchmarking Environment

jupyter-notebook (7.0.0-2)

Jupyter interactive notebook

kalign (1:3.5.1-1+b1)

Global and progressive multiple sequence alignment

kalzium (4:26.04.0-1)

periodic table and chemistry tools

kalzium-data (4:26.04.0-1)

data files for Kalzium

kameleon (2.11.1-1)

Mindful appliance builder

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

king-probe (02.21-1+b2 [arm64], 02.21-1+b1 [loong64, riscv64], 02.21-1 [amd64, armhf, i386, ppc64el, s390x])

Evaluate and visualize protein interatomic packing

kissat (4.0.4-1)

Keep it simple and clean bare metal SAT solver

kissplice (2.6.7-2+b1 [arm64, loong64], 2.6.7-2 [amd64, ppc64el, riscv64])

Detection of various kinds of polymorphisms in RNA-seq data

kleborate (2.4.1-7)

tool to screen Klebsiella genome assemblies

kleborate-examples (2.4.1-7)

tool to screen Klebsiella genome assemblies (example data)

klustakwik (3.0.2+ds-2+b3 [arm64], 3.0.2+ds-2+b2 [riscv64], 3.0.2+ds-2+b1 [loong64], 3.0.2+ds-2 [amd64, armhf, i386, ppc64el, s390x])

automatic sorting of the samples (spikes) into clusters

kma (1.4.21-1+b1 [arm64, loong64], 1.4.21-1 [amd64, ppc64el, riscv64, s390x])

mapping genomic sequences to raw reads directly against redundant databases

kmc (3.2.4+dfsg-1+b5)

count kmers in genomic sequences

kmer (0~20150903+r2013-10)

suite of tools for DNA sequence analysis

kmer-examples (0~20150903+r2013-10)

sample data for kmer suite of tools for DNA sequence analysis

kmerresistance (2.2.0-4+b2 [arm64], 2.2.0-4+b1 [loong64, riscv64], 2.2.0-4 [amd64, ppc64el, s390x])

correlates mapped genes with the predicted species of WGS samples

konclude (0.7.0+1138+git20220514~dfsg-1+b3 [arm64], 0.7.0+1138+git20220514~dfsg-1+b2 [riscv64], 0.7.0+1138+git20220514~dfsg-1+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

tableau-based description logic reasoner for the semantic web

kraken (1.1.1-4+b2 [arm64], 1.1.1-4+b1 [loong64, riscv64], 1.1.1-4 [amd64, ppc64el])

assigning taxonomic labels to short DNA sequences

kraken2 (2.1.3-1+b2 [arm64], 2.1.3-1+b1 [loong64, riscv64], 2.1.3-1 [amd64, armhf, i386, ppc64el, s390x])

taxonomic classification system using exact k-mer matches

kst (2.0.8-7)

scientific data plotting tool

kstars (5:3.6.2-2+b8 [armhf], 5:3.6.2-2+b7 [arm64], 5:3.6.2-2+b6 [amd64, i386, ppc64el, s390x], 5:3.6.2-2+b5 [riscv64], 5:3.6.2-2+b2 [loong64])

desktop planetarium, observation planning and telescope control

kstars-data (5:3.6.2-2)

data files for KStars desktop planetarium

kstars-data-extra-tycho2 (1.1r1-9.2) [non-free]

Tycho-2 star catalog for KStars

lagan (2.0-10+b3 [arm64], 2.0-10+b1 [loong64], 2.0-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

highly parametrizable pairwise global genome sequence aligner

lamarc (2.1.10.1+dfsg-7+b6 [arm64], 2.1.10.1+dfsg-7+b4 [amd64, armhf, i386, ppc64el, s390x], 2.1.10.1+dfsg-7+b3 [riscv64], 2.1.10.1+dfsg-7+b1 [loong64])

Likelihood Analysis with Metropolis Algorithm using Random Coalescence

lamassemble (1.7.4-1)

Merges overlapping "long" DNA reads into a consensus sequences

lambda-align2 (2.0.1-4)

Local Aligner for Massive Biological DatA - v2

lammps (20260211+dfsg1-1)

Molecular Dynamics Simulator

last-align (1651-2)

genome-scale comparison of biological sequences

lastz (1.04.52-1+b1 [arm64, loong64], 1.04.52-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

pairwise aligning DNA sequences

lastz-examples (1.04.52-1)

pairwise aligning DNA sequences (examples and test scripts)

lbt (1.2.2-7+b2 [arm64], 1.2.2-7+b1 [loong64, riscv64], 1.2.2-7 [amd64, armhf, i386, ppc64el, s390x])

converts from LTL formulas to Büchi automata

leaff (0~20150903+r2013-10+b2)

biological sequence library utilities and applications

lexd (1.3.5-3)

Lexicon compiler for non-suffixational morphologies

libatlas-ecmwf-utils (0.46.0-2)

Numerical weather prediction and climate modelling library - utilities

libball1.5-data (1.5.0+git20220524.d85d2dd-5)

Biochemical Algorithms Library (data files)

libbio-db-hts-perl (3.01-6+b1 [loong64], 3.01-6 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Perl interface to the HTS library

libca4.14.4 (7.0.8.1+dfsg1-10)

EPICS channel access client library

libcasadi-dev (3.7.0+ds2-3)

Nonlinear optimization and algorithmic differentiation - development files

libcasadi3.7 (3.7.0+ds2-3)

Nonlinear optimization and algorithmic differentiation

libcg3-1 (1.5.1-2)

Runtime for CG-3

libchemicaltagger-java (1.6.2-4)

tool for semantic text-mining in chemistry

libcom3.23.1 (7.0.8.1+dfsg1-10)

EPICS common library

libdbcsr-dev (2.9.1-1)

Distributed Block Compressed Sparse Row matrix library

libdlpack-dev (1.0-2+b1)

Open In Memory Tensor Structure

libdyssol1.0t64 (1.5.0-1.1)

Tool for dynamic flowsheet simulation - shared libraries

libeccodes-data (2.47.1-2)

GRIB and BUFR enecoding/encoding software library - data

libeckit-utils (2.0.7-2)

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

libfaiss-dev (1.13.2-1+b1)

efficient similarity search and clustering of dense vectors

libfckit-utils (0.14.3-1)

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

libgoby-io-java (3.3.1+dfsg2-12)

IO API for goby

libhdf5-jni (1.14.6+repack-2+b1)

native library used by libhdf5-java

libideep-dev (0.0~git20251020.9275706-1.1)

Intel's mkldnn/dnnl wrapper for pytorch

libifcopenshell-dev (0.8.1+dfsg1-5)

Library for working with Industry Foundation Classes (IFC) data

libifcopenshell0.8.1 (0.8.1+dfsg1-5)

Library for working with Industry Foundation Classes (IFC) data

libinchi-bin (1.07.3+dfsg-2+b1 [loong64], 1.07.3+dfsg-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

International Chemical Identifier (InChI) algorithm (executable)

libjgrapht-java (1.5.2-2)

Java library of graph theory data structures and algorithms

libjgrapht-java

virtual package provided by libjgrapht0.8-java

liblammps-dev (20260211+dfsg1-1)

Molecular Dynamics Simulator (dev files)

liblammps0t64 (20260211+dfsg1-1)

Molecular Dynamics Simulator (shared library)

liblemon-utils (1.3.1+dfsg-7+b1)

Library for Efficient Modeling and Optimization in Networks (utilities)

liblinear-tools (2.3.0+dfsg-5+b3)

Standalone applications for LIBLINEAR

libmcpl-dev (1.3.2-4+b1 [loong64], 1.3.2-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Monte Carlo Particle Lists - development files

libmcpl1 (1.3.2-4+b1 [loong64], 1.3.2-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Monte Carlo Particle Lists - library

libmstoolkit-tools (82-7.2+b1 [arm64, loong64], 82-7.2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

libraries for manipulating mass spectrometry data - tools

libncarg-bin (6.6.2.dfsg.1-12+b2)

NCAR command-language library - development tools

libncarg-data (6.6.2.dfsg.1-12)

NCAR command-language library - Data

libocas-tools (0.97+dfsg-8+b3)

Standalone applications implementing the OCAS solver

libonnx-dev (1.20.0-5)

Open Neural Network Exchange (ONNX) (dev)

libonnx-testdata (1.20.0-5)

Open Neural Network Exchange (ONNX) (test data)

liboscar4-java (5.3.0+dfsg-1)

automated annotation of chemistry in scientific articles

libpappsomspp-cli (0.11.15-3)

C++ library to handle mass spectrometry data (GUI development files)

libphitsmcpl1 (1.3.2-4+b1 [loong64], 1.3.2-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Monte Carlo Particle Lists - PHITS library

libpluto-jpl-eph-dev (0.0~git20240106.0c2782e-1)

development files to interact with JPL ephemerides data

libpluto-lunar-dev (0.0~git20180825.e34c1d1-1+b2 [arm64, loong64], 0.0~git20180825.e34c1d1-1+b1 [amd64, riscv64], 0.0~git20180825.e34c1d1-1 [armhf, i386, ppc64el, s390x])

development files for astronomical Lunar library

libqgis-customwidgets (3.44.11+dfsg-1)

QGIS custom widgets for Qt Designer

libsigmf (1.0.2-4+b1)

SigMF data format handling library

libsilo-bin (4.11-6.1+b5)

Utilities to manipulate libsilo files

libsmiles-scripts-java (0.4.0+dfsg-3)

command line tools to handle SMILES descriptors - Java libraries

libsmiles-scripts-perl (0.4.0+dfsg-3)

command line tools to handle SMILES descriptors - Perl libraries

libssm-bin (1.4.0-2+b4)

macromolecular superposition library - binaries

libsswmcpl1 (1.3.2-4+b1 [loong64], 1.3.2-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Monte Carlo Particle Lists - SSW library

libtorch-test (2.12.0+dfsg2-4)

Tensors and Dynamic neural networks in Python (Test Binaries)

libtrexio0 (2.2.3-3+b4)

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

libuhd4.9.0-dpdk-tests (4.9.0.1-1.3)

universal hardware driver for Ettus Research products - DPDK tests

libvcflib-tools (1.0.12+dfsg-2)

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+b1 [arm64, loong64], 3.1.0+ds-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Maximally Localized Wannier Functions - development library

libxgboost-predictor-java (0.3.1+dfsg-3)

Java implementation of XGBoost predictor for online prediction tasks

libxy-bin (1.6-3.1+b5)

xylib - utilities

liggghts (3.8.0+repack1-14+b1)

Open Source DEM Particle Simulation Software.

lighter (1.1.3-1+b1 [arm64, loong64], 1.1.3-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast and memory-efficient sequencing error corrector

litl-tools (0.2-3+b2)

Lightweight Trace Library - tools

llama.cpp (9413+dfsg-1)

LLM inference in C/C++ - metapackage

llama.cpp-examples (9413+dfsg-1)

LLM inference in C/C++ - example programs

llama.cpp-tests (9413+dfsg-1)

LLM inference in C/C++ - tests

llama.cpp-tools (9413+dfsg-1)

LLM inference in C/C++ - main utilities

llama.cpp-tools-extra (9413+dfsg-1)

LLM inference in C/C++ - extra utilities

llm (0.30-1)

CLI utility and Python library for interacting with Large Language Models

loki (2.4.7.4-12+b1 [arm64, loong64], 2.4.7.4-12 [amd64, armhf, i386, ppc64el, riscv64, s390x])

MCMC linkage analysis on general pedigrees

looktxt (1.4.1-3+b2 [arm64], 1.4.1-3+b1 [loong64, riscv64], 1.4.1-3 [amd64, armhf, i386, ppc64el, s390x])

Convert free format text file into scientific data formats

looptools (2.16-2+b1)

Integral Evaluator of One-loop Feynman Diagram

lorene (0.0.0~cvs20161116+dfsg-2)

framework for numerical relativity

lorene-codes-src (0.0.0~cvs20161116+dfsg-2)

source files of LORENE-based codes

lttoolbox-dev (3.8.3-2)

Development tools and library for lttoolbox

lua-cnrun (2.1.0-4+b1 [loong64], 2.1.0-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

NeuroML-capable neuronal network simulator (Lua package)

lucy (1.20-6+b1 [arm64, loong64], 1.20-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

DNA sequence quality and vector trimming tool

lumpy-sv (0.3.1+dfsg-8.1+b1 [loong64], 0.3.1+dfsg-8.1 [amd64, arm64, armhf, i386, ppc64el, riscv64])

general probabilistic framework for structural variant discovery

lumpy-sv-examples (0.3.1+dfsg-8.1)

general probabilistic framework for structural variant discovery (data)

lutefisk (1.0.7+dfsg-7+b2 [arm64], 1.0.7+dfsg-7+b1 [loong64, riscv64], 1.0.7+dfsg-7 [amd64, armhf, i386, ppc64el, s390x])

de novo interpretation of peptide CID spectra

lxi-tools (2.8-2)

LAN eXtensions for Instrumentation (LXI) software interface

m2kcli (0.9.0-4+b1 [loong64], 0.9.0-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

ADI tool for interfacing with the ADALM2000

macs (3.0.2-3)

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

macsyfinder (2.1.6-1)

detection of macromolecular systems in protein datasets

maffilter (1.3.1+dfsg-7+b2 [arm64], 1.3.1+dfsg-7+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

process genome alignment in the Multiple Alignment Format

maffilter-examples (1.3.1+dfsg-7)

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

mafft (7.525-1+b1 [arm64, loong64], 7.525-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Multiple alignment program for amino acid or nucleotide sequences

mandelbrot-solver (3.2.3-1+b2)

Solver for Mandelbrot polynomials based on MPSolve

mapdamage (2.2.3+dfsg-3)

tracking and quantifying damage patterns in ancient DNA sequences

maq (0.7.1-10+b1 [arm64, loong64], 0.7.1-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

maqview (0.2.5-12+b1 [arm64, loong64], 0.2.5-12 [amd64, armhf, i386, ppc64el, riscv64, s390x])

graphical read alignment viewer for short gene sequences

mash (2.3+dfsg-6+b4 [arm64, riscv64], 2.3+dfsg-6+b3 [amd64, ppc64el, s390x], 2.3+dfsg-6+b1 [loong64])

fast genome and metagenome distance estimation using MinHash

massxpert2 (10.4.4-1)

transitional package for massxpert2 -> massxpert3

massxpert2-data (10.4.4-1)

transitional package for massxpert2-dat -> massxpert3-data

massxpert3 (10.4.4-1)

polymer chemistry modelling and mass spectrometry data simulation (runtime)

massxpert3-data (10.4.4-1)

polymer chemistry modelling and mass spectrometry data simulation (data)

matlab-brain2mesh (0.7.9-3) [contrib]

automated brain tetrahedral mesh generation toolbox for MATLAB

matlab-gdf (0.1.3-16) [contrib]

IO library for the GDF -- Matlab interface

matlab-iso2mesh (1.9.8+ds-3) [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 (2.9.8-3) [contrib]

native JSON/UBJSON/MassagePack encoder/decoder for MATLAB

matlab-zmat (1.0.0+ds-1) [contrib]

in-memory data compression for MATLAB

maude (3.5.1-1+b1 [arm64, loong64], 3.5.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

high-performance logical framework

mauve-aligner (2.4.0+4736-6)

multiple genome alignment

mayo (0.9.0+git20251225+ds-3)

3D CAD viewer and converter based on Qt + OpenCascade

mbpoll (1.5.2-2+b1 [arm64, loong64], 1.5.2-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

mbt (3.11-2+b2)

memory-based tagger-generator and tagger

mbtserver (0.17-2+b2 [arm64], 0.17-2+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Server extensions for the MBT tagger

mcaller (1.0.3+git20210624.b415090-3)

find methylation in nanopore reads

mcpl (1.3.2-4+b1 [loong64], 1.3.2-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Monte Carlo Particle Lists - libraries and tools

mcstas (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation

mcstas-clusterscripts (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - parallelization scripts

mcstas-comps (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - components

mcstas-manuals (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - documentation

mcstas-mccodelib (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - Python code library

mcstas-mcdisplay-mantid (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - Mantid instrument display

mcstas-mcdisplay-matlab (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - Matlab/Octave instrument display

mcstas-mcdisplay-matplotlib (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - Matplotlib instrument display

mcstas-mcdisplay-pyqtgraph (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - pyqtgraph instrument display

mcstas-mcdisplay-webgl (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - WebGL instrument display

mcstas-mcdisplay-webgl-classic (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - WebGL instrument display

mcstas-mcdoc (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - documentation browser

mcstas-mcgui (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - GUI

mcstas-mcplot-html (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - HTML plotting frontend

mcstas-mcplot-matlab (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - Matlab/Octave plotting frontend

mcstas-mcplot-matplotlib (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - Matplotlib plotting frontend

mcstas-mcplot-pyqtgraph (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - pyqtgraph plotting frontend

mcstas-mcresplot (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - resolution function plotter

mcstas-mcrun (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - runner

mcstas-suite-python (3.5+3.5.19+ds5-3)

Neutron ray-trace simulation - full simulation suite

mcxtrace (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation

mcxtrace-clusterscripts (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - parallelization scripts

mcxtrace-comps (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - components

mcxtrace-manuals (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - documentation

mcxtrace-mccodelib (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - Python code library

mcxtrace-mxdisplay-matlab (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - Matlab/Octave instrument display

mcxtrace-mxdisplay-matplotlib (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - Matplotlib instrument display

mcxtrace-mxdisplay-pyqtgraph (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - pyqtgraph instrument display

mcxtrace-mxdisplay-webgl (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - WebGL instrument display

mcxtrace-mxdisplay-webgl-classic (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - WebGL instrument display

mcxtrace-mxdoc (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - documentation browser

mcxtrace-mxgui (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - GUI

mcxtrace-mxplot-html (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - HTML plotting frontend

mcxtrace-mxplot-matlab (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - Matlab/Octave plotting frontend

mcxtrace-mxplot-matplotlib (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - Matplotlib plotting frontend

mcxtrace-mxplot-pyqtgraph (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - pyqtgraph plotting frontend

mcxtrace-mxrun (3.5+3.5.19+ds5-3)

X-ray ray-trace simulation - runner

mcxtrace-suite-python (3.5+3.5.19+ds5-3)

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 (1.29.0-2+b1 [arm64, loong64], 1.29.0-2 [amd64, ppc64el, riscv64, s390x])

software package for FDTD simulation

meep-mpi-default (1.29.0-2+b2)

software package for FDTD simulation, parallel version

megadepth (1.2.0-5+b2 [arm64], 1.2.0-5+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

computes coverage from BigWig and BAM sequencing files

megahit (1.2.9+dfsg-1)

ultra-fast and memory-efficient meta-genome assembler

melting (5.2.0-3)

compute the melting temperature of nucleic acid duplex

merkaartor (0.20.0+ds-3+b2)

map editor for OpenStreetMap.org

meryl (0~20150903+r2013-10+b2)

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

metaeuk (7-bba0d80+ds-2+b2 [arm64], 7-bba0d80+ds-2+b1 [amd64, loong64, ppc64el, riscv64])

sensitive, high-throughput gene discovery and annotation for metagenomics

metaeuk-examples (7-bba0d80+ds-2)

optional resources for the metaeuk package

metaphlan (4.0.4+ds-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 (2.0.1-9)

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 (5.26.3-6)

Interactive data visualization and analysis environment,

metview-data (5.26.3-6)

Data needed for the Metview data analysis environment

mhap (2.1.3+dfsg-3)

locality-sensitive hashing to detect long-read overlaps

mia-doctools (2.4.7-18)

Helper scripts for run-time document creation

mia-tools (2.4.7-18+b1)

Command line tools for gray scale image processing

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 (5.3.5+repack-1)

hardware & software framework to learn microcontrollers

minc-tools (2.3.00+dfsg-17)

MNI medical image format tools

minexpert2 (11.4.2-2.1)

transitional package for minexpert2 -> minexpert3

minexpert3 (11.4.2-2.1)

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

minia (3.2.6-5+b1 [arm64, loong64], 3.2.6-5 [amd64, ppc64el, riscv64])

short-read biological sequence assembler

miniasm (0.3+dfsg-4+b2 [arm64], 0.3+dfsg-4+b1 [loong64, riscv64], 0.3+dfsg-4 [amd64, armhf, i386, ppc64el, s390x])

ultrafast de novo assembler for long noisy DNA sequencing reads

minicondor (25.10.1+dfsg-2)

distributed workload management system - single node configuration

minimac4 (4.1.6-2)

Fast Imputation Based on State Space Reduction HMM

minimap (0.2-8+b4)

tool for approximate mapping of long biosequences such as DNA reads

minimap2 (2.27+dfsg-1+b5 [arm64], 2.27+dfsg-1+b4 [amd64, armhf, i386, ppc64el, riscv64, s390x], 2.27+dfsg-1+b1 [loong64])

versatile pairwise aligner for genomic and spliced nucleotide sequences

minisat (1:2.2.1-8+b3 [arm64], 1:2.2.1-8+b1 [loong64], 1:2.2.1-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Fast and lightweight SAT solver

minisat+ (1.0-5+b1 [loong64], 1.0-5 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

solver for pseudo-Boolean constraints

mipe (1.1-9)

Tools to store PCR-derived data

mira-assembler (4.9.6-12+b1)

Whole Genome Shotgun and EST Sequence Assembler

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

extract of RFAM 12 rRNA database

mirtop (0.4.30-1)

annotate miRNAs with a standard mirna/isomir naming

missfits (2.8.0-6+b1 [arm64, loong64], 2.8.0-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Basic maintenance and packaging tasks on FITS files

mitools (2.0.5-9+b2)

view, convert and perform basic maths with medical image datasets

mlv-smile (1.47-10+b1 [arm64, loong64], 1.47-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Find statistically significant patterns in sequences

mmb (4.2+dfsg-2+b1)

model the structure and dynamics of macromolecules

mmb-common (4.2+dfsg-2)

model the structure and dynamics of macromolecules (common files)

mmmulti (0.1-4+b1 [arm64, loong64], 0.1-4 [amd64, riscv64])

memory backed multimap

mmseqs2 (18-8cc5c+ds-1+b2 [arm64], 18-8cc5c+ds-1+b1 [amd64, loong64, ppc64el, riscv64])

ultra fast and sensitive protein search and clustering

mmseqs2-examples (18-8cc5c+ds-1)

optional resources for the mmseqs2 package

mocassin (2.02.73.2-1+b2 [arm64, loong64], 2.02.73.2-1+b1 [riscv64], 2.02.73.2-1 [amd64, armhf, i386, 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 (0.3.1-3)

Semi-empirical electronic structure and molecular dynamics

molequeue (0.9.0-3+b1)

Desktop integration of high performance computing resources

mona (1.4-18-1+b3 [arm64], 1.4-18-1+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

theorem prover based on automata

montage (6.1+dfsg-2+b2 [loong64], 6.1+dfsg-2+b1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Toolkit for assembling FITS images into mosaics

montage-gridtools (6.1+dfsg-2+b2 [loong64], 6.1+dfsg-2+b1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Create files to run montage on the grid

mopac (23.2.5-1)

Molecular Orbital PACkage (MOPAC)

mopac7-bin (1.15-7+b1 [arm64, loong64], 1.15-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Semi-empirical Quantum Chemistry Library (binaries)

mosdepth (0.3.11+ds-3+b1 [loong64], 0.3.11+ds-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

BAM/CRAM depth calculation biological sequencing

mosdepth-examples (0.3.11+ds-3)

Test data for mosdepth

mothur (1.48.5-2)

sequence analysis suite for research on microbiota

mpb (1.12.0-1+b1 [arm64], 1.12.0-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

MIT Photonic-Bands

mpb-mpi (1.12.0-1+b1 [arm64], 1.12.0-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

MIT Photonic-Bands, parallel (mpich) version

mpb-scm (1.12.0-1)

MIT Photonic-Bands initialisation files

mpgrafic (0.3.19-1+b6 [arm64, s390x], 0.3.19-1+b5 [amd64, armhf, i386, ppc64el], 0.3.19-1+b4 [riscv64])

MPI version of N-body initial conditions grafic package

mpsolve (3.2.3-1+b2)

Multiprecision polynomial solver (command line version)

mptp (0.2.5-2+b1 [arm64, loong64], 0.2.5-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

single-locus species delimitation

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 (1:2.15.14+ds-1)

Mobile Robot Programming Toolkit - Console and GUI applications

mrpt-common (1:2.15.14+ds-1)

Mobile Robot Programming Toolkit - Example datasets and files

mrtrix3 (3.0.8-1)

diffusion-weighted MRI white matter tractography

mseed2sac (2.3+ds1-1+b2 [arm64, loong64], 2.3+ds1-1+b1 [riscv64], 2.3+ds1-1 [amd64, armhf, i386, ppc64el, s390x])

Convert MiniSEED time series data to SAC

mssstest (3.0-8) [non-free]

Normalisation of disease scores for patients with Multiple Sclerosis

multiqc (1.21+dfsg-4)

output integration for RNA sequencing across tools and samples

mummer (3.23+dfsg-8+b3 [arm64], 3.23+dfsg-8+b2 [riscv64], 3.23+dfsg-8+b1 [loong64], 3.23+dfsg-8 [amd64, armhf, i386, ppc64el, s390x])

Efficient sequence alignment of full genomes

munipack (0.6.2-1)

Astronomical photometry software package

munipack-cli (0.6.2-1+b1 [arm64], 0.6.2-1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Command line interface of Munipack

munipack-core (0.6.2-1+b1 [arm64], 0.6.2-1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Core routines of Munipack

munipack-gui (0.6.2-1+b1 [arm64], 0.6.2-1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Graphical user interface of Munipack

muscle (1:5.1.0-1+b2 [arm64, loong64], 1:5.1.0-1+b1 [riscv64], 1:5.1.0-1 [amd64, armhf, i386, ppc64el, s390x])

Multiple alignment program of protein sequences

muscle3 (3.8.1551-3+b2 [arm64], 3.8.1551-3+b1 [loong64], 3.8.1551-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

multiple alignment program of protein sequences

music-bin (1.2.1-0.7+b1 [arm64], 1.2.1-0.7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Multi-Simulation Coordinator for MPI -- Utilities

mustang (3.2.4-1+b2 [arm64], 3.2.4-1+b1 [loong64, riscv64], 3.2.4-1 [amd64, armhf, i386, 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+b2 [riscv64], 1.2.0-4+b1 [loong64], 1.2.0-4 [amd64, arm64, armhf, i386, ppc64el, s390x])

remove lambda phage reads from a fastq file

nanopolish (0.14.0-3)

consensus caller for nanopore sequencing data

nanopub (0.2.0+ds-1.1+b1)

CLI tool to sign nanopublications

nanostat (1.4.0-4)

statistics on long biological sequences

nanosv (1.2.4+git20190409.c1ae30c-7)

structural variant caller for nanopore data

nast-ier (20101212+dfsg1-6+b2 [arm64], 20101212+dfsg1-6+b1 [loong64], 20101212+dfsg1-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

NAST-based DNA alignment tool

nautic (1.5-7)

computation of observer position in astro-navigation

ncbi-acc-download (0.2.8-3)

download genome files from NCBI by accession

ncbi-blast+ (2.17.0+ds-7)

next generation suite of BLAST sequence search tools

ncbi-blast+-legacy (2.17.0+ds-7)

NCBI Blast legacy call script

ncbi-cn3d (3.0.20170106+dfsg2-7+b1)

3-dimensional viewer for biological molecules

ncbi-entrez-direct (24.0.20250523+dfsg-2+b2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x], 24.0.20250523+dfsg-2+b1 [loong64])

NCBI Entrez utilities on the command line

ncbi-epcr (2.3.12-1-11+b1 [arm64, loong64], 2.3.12-1-11 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

ncbi-rrna-data (6.1.20170106+dfsg2-7)

large rRNA BLAST databases distributed with the NCBI toolkit

ncbi-seg (0.0.20000620-8+b1 [arm64, loong64], 0.0.20000620-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

ncbi-tools-bin (6.1.20170106+dfsg2-7+b1)

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11 (6.1.20170106+dfsg2-7+b1)

NCBI libraries for biology applications (X-based utilities)

ncl-ncarg (6.6.2.dfsg.1-12+b2)

NCAR Command Language and NCAR graphics

ncl-tools (2.1.21+git20210811.b1213a7-6+b2)

tools to deal with NEXUS files

nco (5.3.9-1)

Command-line operators to analyze netCDF files

ncoils (2002-10+b1 [arm64, loong64], 2002-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

coiled coil secondary structure prediction

neat (2.3.2-2+b4 [arm64], 2.3.2-2+b3 [amd64, i386, s390x], 2.3.2-2+b2 [armhf, ppc64el, riscv64], 2.3.2-2+b1 [loong64])

Nebular Empirical Analysis Tool

neobio (0.0.20030929-6)

computes alignments of amino acid and nucleotide sequences

netcdf-bin (1:4.10.0-1)

Programs for reading and writing NetCDF files

neurodebian (0.43.1)

neuroscience-oriented distribution - repository configuration

neurodebian-archive-keyring (0.43.1)

neuroscience-oriented distribution - GnuPG archive keys

neurodebian-desktop (0.43.1)

neuroscience-oriented distribution - desktop integration

neurodebian-dev (0.43.1)

neuroscience-oriented distribution - development tools

neurodebian-freeze (0.43.1)

nd_freeze tool to freeze APT sources to use snapshots

neurodebian-popularity-contest (0.43.1)

neuroscience-oriented distribution - popcon integration

neuron (8.2.6-3)

Simulation environment for computational models of neurons

neuron-dev (8.2.6-3)

Neuron simulation environment - Development files

nexus-tools (4.4.3-10+b1)

NeXus scientific data file format - applications

ngmlr (0.2.7+git20210816.a2a31fb+dfsg-4+b1 [loong64], 0.2.7+git20210816.a2a31fb+dfsg-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

CoNvex Gap-cost alignMents for Long Reads

nim-kexpr-dev (0.0.2-4)

kexpr math expressions for nim

nim-lapper-dev (0.1.8-1)

simple, fast interval searches for nim

njplot (2.4-9+b3 [arm64], 2.4-9+b2 [riscv64], 2.4-9+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

phylogenetic tree drawing program

nmodl (0.6-4)

Code generation engine for the NEURON modeling language

norsnet (1.0.17-8)

tool to identify unstructured loops in proteins

norsp (1.0.6-8)

predictor of non-regular secondary structure

ntcard (1.2.2+dfsg-10+b1 [arm64, loong64], 1.2.2+dfsg-10 [amd64, ppc64el, riscv64, s390x])

Streaming algorithm to estimate cardinality in genomics datasets

nthash (2.3.0+dfsg-5+b1 [arm64, loong64], 2.3.0+dfsg-5 [amd64, ppc64el, riscv64, s390x])

Methods to evaluate runtime and uniformity tests for hashing methods

numdiff (5.9.0-2+b1 [arm64, loong64], 5.9.0-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Compare similar files with numeric fields

nutsqlite (2.0.6-4)

Dietary nutrition analysis software

nwchem (7.3.1-1)

High-performance computational chemistry software (default MPI)

nwchem-data (7.3.1-1)

High-performance computational chemistry software (data files)

nwchem-mpich (7.3.1-1)

High-performance computational chemistry software (MPICH build)

nwchem-openmpi (7.3.1-1)

High-performance computational chemistry software (OpenMPI build)

nxtrim (0.4.3+dfsg-6+b1 [arm64, loong64], 0.4.3+dfsg-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Optimized trimming of Illumina mate pair reads

oar-common (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler common package

oar-node (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler node package

oar-server (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler server package

oar-server-mysql (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler MySQL server backend package

oar-server-pgsql (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler PostgreSQL server backend package

oar-user (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler user package

oar-user-mysql (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler MySQL user backend package

oar-user-pgsql (2.6.1-1+b1 [arm64, loong64], 2.6.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OAR batch scheduler PostgreSQL user backend package

oar-web-status (2.6.1-1)

OAR batch scheduler visualization tool package

occt-draw (7.9.2+dfsg-4)

Open CASCADE Technology command interpreter and graphical test system

octave-bart (1.0.00-2)

Octave bindings for BART

octave-biosig (3.9.5-1)

Octave bindings for BioSig library

octave-brain2mesh (0.7.9-3)

automated brain tetrahedral mesh generation toolbox for Octave

octave-gdf (0.1.3-16)

IO library for the GDF -- Octave interface

octave-iso2mesh (1.9.8+ds-3)

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 (2.9.8-3)

native JSON/UBJSON/MassagePack encoder/decoder for Octave

octave-psychtoolbox-3 (3.0.22.2+dfsg-3)

toolbox for vision research -- Octave bindings

octave-zmat (1.0.0+ds-1)

in-memory data compression for Octave

octomap-tools (1.10.0+dfsg-3+b1)

Tools for 3D occupancy grid mapping

octovis (1.10.0+dfsg-3+b1)

Visualization tool for OctoMap

odil (0.13.0-3)

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

odin (2.0.5-9+b2)

develop, simulate and run magnetic resonance sequences

onnxruntime-tools (1.23.2+dfsg-6)

cross-platform inference and training ML accelerator (tools)

ont-fast5-api (4.1.3+dfsg-5)

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

openbabel (3.1.1+dfsg-14+b1 [loong64], 3.1.1+dfsg-14 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Chemical toolbox utilities (cli)

openbabel-gui (3.1.1+dfsg-14+b1 [loong64], 3.1.1+dfsg-14 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Chemical toolbox utilities (graphical user interface)

opendrop (3.3.2-3+b2 [i386], 3.3.2-3+b1 [amd64, arm64, armhf, ppc64el, riscv64, s390x])

fully-featured pendant drop tensiometry software

openstructure (2.11.1-3)

Open-Source Computational Structural Biology Framework

opentelemetry-proto (1.8.0-3)

OpenTelemetry protocol specification and proto files

openturns-common (1.27.1-1)

generic tool to treat and quantify uncertainties (common files)

openuniverse (1.0beta3.1+dfsg-7.2+b1 [arm64, loong64], 1.0beta3.1+dfsg-7.2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

3D Universe Simulator

openuniverse-common (1.0beta3.1+dfsg-7.2)

3D Universe Simulator data files

optgeo (3.03-1)

simulator for geometrical optics

opticalraytracer (9.6-5)

Virtual lens/mirror design workshop

optimir (1.2-2)

Integrating genetic variations in miRNA alignment

orthanc (1.12.11+dfsg-7)

Lightweight, RESTful DICOM server for medical imaging

orthanc-dicomweb (1.23+dfsg-2)

Plugin to extend Orthanc with support of WADO and DICOMweb

orthanc-gdcm (1.8+dfsg-3)

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

orthanc-imagej (1.2+dfsg-6)

ImageJ plugin to import images from Orthanc

orthanc-mysql (5.0+dfsg-6)

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

orthanc-neuro (1.1+dfsg-3)

Neuroimaging plugin for Orthanc

orthanc-postgresql (5.0+dfsg-7)

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

orthanc-python (7.1+ds-1)

Develop plugins for Orthanc using the Python programming language

orthanc-webviewer (2.10+dfsg-3)

Web viewer of medical images for Orthanc

orthanc-wsi (3.3+dfsg-6)

Whole-slide imaging support for Orthanc (digital pathology)

oscar (1.7.1-1)

Open Source CPAP Analysis Reporter (OSCAR)

osra (2.2.4-1)

optical structure recognition

osrm-backend (26.5.0+dfsg1-2)

Open Source Routing Machine - high performance routing engine

osrm-backend-service (26.5.0+dfsg1-2)

Open Source Routing Machine - systemd service

otf-trace (1.12.5+dfsg-8+b6)

Open Trace Format support library - development files

otf2-tools (3.1.1-4+b1)

Open Trace Format support library - tools

ovito (3.15.4~ds-1)

Scientific data visualization and analysis software for atomistic and molecular

oxrq (0.1.0+ds-2+b1)

CLI tool for running SPARQL queries over RDF data

packmol (1:21.2.3-1)

Initial configurations for Molecular Dynamics Simulations

paje.app (1.98-2+b2 [arm64], 1.98-2+b1 [amd64, armhf, i386, ppc64el, riscv64, s390x], 1.98-2 [loong64])

generic visualization tool (Gantt chart and more)

pal2nal (14.1-3)

converts proteins to genomic DNA alignment

paleomix (1.3.10-1)

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

paml (4.9j+dfsg-6+b1 [arm64, loong64], 4.9j+dfsg-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Phylogenetic Analysis by Maximum Likelihood (PAML)

pan-config (0.4)

PAN Blend config package

pan-tasks (0.4)

PAN Blends tasks for tasksel

paraclu (10-1+b2 [arm64], 10-1+b1 [loong64, riscv64], 10-1 [amd64, armhf, i386, ppc64el, s390x])

Parametric clustering of genomic and transcriptomic features

parafly (0.1.0-5+b2 [loong64], 0.1.0-5+b1 [arm64], 0.1.0-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

parallel command processing using OpenMP

parallel-fastq-dump (0.6.7-3)

parallel fastq-dump wrapper

paraview (6.0.1+dfsg1-8)

Parallel Visualization Application

parsinsert (1.04-17+b1 [loong64], 1.04-17 [amd64, arm64, i386, ppc64el, riscv64, s390x])

Parsimonious Insertion of unclassified sequences into phylogenetic trees

parsinsert-testdata (1.04-17)

Test data for parsinsert

parsnp (2.1.3+dfsg-1+b1 [arm64, loong64], 2.1.3+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

rapid core genome multi-alignment

patman (1.2.2+dfsg-8+b3 [arm64], 1.2.2+dfsg-8+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

rapid alignment of short sequences to large databases

pbbamtools (2.4.0+dfsg-4)

processing Pacific Biosciences binary alignment/map files

pbdagcon (0.3+git20180411.c14c422+dfsg-10)

sequence consensus using directed acyclic graphs

pbsim (1.0.3+git20180330.e014b1d+dfsg-3+b2 [arm64], 1.0.3+git20180330.e014b1d+dfsg-3+b1 [loong64, riscv64], 1.0.3+git20180330.e014b1d+dfsg-3 [amd64, armhf, i386, ppc64el, s390x])

simulator for PacBio sequencing reads

pdb-tools (2.6.0-1)

tools for manipulating and editing PDB files

pdb2pqr (3.6.1+dfsg-2)

Preparation of protein structures for electrostatics calculations

perlprimer (1.2.4-2)

Graphical design of primers for PCR

perm (0.4.0-8+b3 [arm64], 0.4.0-8+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

efficient mapping of short reads with periodic spaced seeds

persalys (20.0+ds-3)

GUI for uncertainty treatment and variabilities management

pftools (3.2.12-3)

build and search protein and DNA generalized profiles

phast (1.8+dfsg-1+b1 [arm64, loong64], 1.8+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

phylogenetic analysis with space/time models

phipack (0.0.20160614-5+b2 [arm64], 0.0.20160614-5+b1 [loong64, riscv64], 0.0.20160614-5 [amd64, armhf, i386, ppc64el, s390x])

PHI test and other tests of recombination

phybin (0.3-7+b2 [loong64], 0.3-7+b1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

binning/clustering newick trees by topology

phylip (1:3.697+dfsg-4+b2 [arm64], 1:3.697+dfsg-4+b1 [loong64], 1:3.697+dfsg-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

package of programs for inferring phylogenies

phylonium (1.7-3+b2 [arm64], 1.7-3+b1 [loong64], 1.7-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Fast and Accurate Estimation of Evolutionary Distances

phyml (3:3.3.20250515-2)

Phylogenetic estimation using Maximum Likelihood

physamp (1.1.0-6+b1 [arm64, loong64], 1.1.0-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

sample sequence alignment corresponding to phylogeny

phyutility (2.7.3+dfsg-4+b1 [loong64, riscv64], 2.7.3+dfsg-4 [amd64, arm64, armhf, i386, ppc64el, s390x])

simple analyses or modifications on both phylogenetic trees and data matrices

phyx (1.3.2+ds-1+b2 [arm64], 1.3.2+ds-1+b1 [amd64, armhf, i386, ppc64el, riscv64, s390x], 1.3.2+ds-1 [loong64])

UNIX-style phylogenetic analyses on trees and sequences

picard-tools (3.4.0+dfsg-1)

Command line tools to manipulate SAM and BAM files

picopore (1.2.0-3)

lossless compression of Nanopore files

picosat (965-3+b1 [loong64], 965-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

SAT solver with proof and core support

piler (0~20140707-4+b2 [arm64], 0~20140707-4+b1 [loong64], 0~20140707-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

genomic repeat analysis

pilercr (1.06+dfsg-5+b2 [arm64], 1.06+dfsg-5+b1 [loong64, riscv64], 1.06+dfsg-5 [amd64, armhf, i386, ppc64el, s390x])

software for finding CRISPR repeats

pilon (1.24-4)

automated genome assembly improvement and variant detection tool

pinfish (0.1.0+ds-4+b10 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x], 0.1.0+ds-4+b1 [loong64])

Collection of tools to annotate genomes using long read transcriptomics data

pinfish-examples (0.1.0+ds-4)

Examples and test data for pinfish

pirs (2.0.2+dfsg-13)

Profile based Illumina pair-end Reads Simulator

pirs-examples (2.0.2+dfsg-13)

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

pirs-profiles (2.0.2+dfsg-13)

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

pkg-r-autopkgtest (20250812)

Script for the automatic testing of R packages

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+b5 [amd64, arm64, ppc64el, s390x], 0.1.13-23+b4 [armhf, i386, riscv64], 0.1.13-23+b2 [loong64])

Gravitation simulation of planetary bodies

plasmidid (1.6.5+dfsg-2)

mapping-based, assembly-assisted plasmid identification tool

plasmidseeker (1.3+dfsg-3+b2)

identification of known plasmids from whole-genome sequencing reads

plast (2.3.2+dfsg-12+b2 [arm64], 2.3.2+dfsg-12+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Parallel Local Sequence Alignment Search Tool

plast-example (2.3.2+dfsg-12)

Parallel Local Sequence Alignment Search Tool (example data)

plastimatch (1.10.0+dfsg.2-1+b1)

medical image reconstruction and registration

plink (1.07+dfsg-5+b1 [arm64, loong64], 1.07+dfsg-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

whole-genome association analysis toolset

plink1.9 (1.90~b7.7-241022-2+b2 [arm64], 1.90~b7.7-241022-2+b1 [amd64, armhf, i386])

whole-genome association analysis toolset

plink2 (2.00~a6.9-250129+dfsg-1+b3 [arm64], 2.00~a6.9-250129+dfsg-1+b2 [amd64, armhf, i386, ppc64el, riscv64, s390x], 2.00~a6.9-250129+dfsg-1+b1 [loong64])

whole-genome association analysis toolset

plus42 (1.3.15+ds-1)

advanced scientific calculator based on the HP-42S

pluto-jpl-eph (0.0~git20240106.0c2782e-1)

command line handling of JPL ephemerides data

pluto-lunar (0.0~git20180825.e34c1d1-1+b2 [arm64, loong64], 0.0~git20180825.e34c1d1-1+b1 [amd64, riscv64], 0.0~git20180825.e34c1d1-1 [armhf, i386, ppc64el, s390x])

routines for predictions of positions in solar system

pnetcdf-bin (1.14.1-2+b2)

Programs for reading and writing parallel NetCDF files

poa (2.0+20060928-10+b1 [arm64, loong64], 2.0+20060928-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Partial Order Alignment for multiple sequence alignment

populations (1.2.33+svn0120106+dfsg-8+b1 [arm64, loong64], 1.2.33+svn0120106+dfsg-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

population genetic software

porechop (0.2.4+dfsg-9)

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 (6.4.64+dfsg-1)

program for speech analysis and synthesis

prank (250331-1+b1 [arm64, loong64], 250331-1 [amd64, armhf, i386, ppc64el, riscv64, 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 (1.0.11-14+b1)

bayesian estimation of gene trees taking the species tree into account

primer3 (2.6.1-6+b1 [arm64, loong64], 2.6.1-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

tool to design flanking oligo nucleotides for DNA amplification

primer3-examples (2.6.1-6)

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+b1 [loong64], 0.603-6 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

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+b2 [arm64], 1.4-10+b1 [loong64, riscv64], 1.4-10 [amd64, armhf, i386, ppc64el, s390x])

multiple sequence alignment using partition function posterior probabilities

probcons (1.12-15+b1 [arm64, loong64], 1.12-15 [amd64, armhf, i386, ppc64el, riscv64, s390x])

PROBabilistic CONSistency-based multiple sequence alignment

probcons-extra (1.12-15+b1 [arm64, loong64], 1.12-15 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Extra programs from the probcons package

proda (1.0-14+b2 [arm64], 1.0-14+b1 [loong64], 1.0-14 [amd64, armhf, i386, ppc64el, riscv64, s390x])

multiple alignment of protein sequences

prodigal (1:2.6.3-6+b2 [arm64], 1:2.6.3-6+b1 [loong64, riscv64], 1:2.6.3-6 [amd64, armhf, i386, 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+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for profbval

profnet-chop (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for profchop

profnet-con (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for profcon

profnet-isis (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for profisis

profnet-md (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for metadisorder

profnet-norsnet (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for norsnet

profnet-prof (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for profacc

profnet-snapfun (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for snapfun

profphd-net (1.0.22-8+b2 [arm64], 1.0.22-8+b1 [loong64, riscv64], 1.0.22-8 [amd64, armhf, i386, ppc64el, s390x])

neural network architecture for profphd

profphd-utils (1.0.10-7+b2 [arm64], 1.0.10-7+b1 [loong64, riscv64], 1.0.10-7 [amd64, armhf, i386, ppc64el, s390x])

profphd helper utilities convert_seq and filter_hssp

proftmb (1.1.12-11+b2 [arm64, riscv64], 1.1.12-11+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

per-residue prediction of bacterial transmembrane beta barrels

progressivemauve (1.2.0+4713+dfsg-6+b1)

multiple genome alignment algorithms

proj-bin (9.8.1-1)

Cartographic projection library (tools)

prokka (1.14.6+dfsg-6)

rapid annotation of prokaryotic genomes

prometheus-sensor-exporter (0.1.0-2)

Prometheus exporter for I²C temperature and humidity sensors

promod3 (3.6.0+ds-1)

protein homology modelling engine

promod3-data (3.6.0+ds-1)

protein homology modelling engine - data files

proteinortho (6.3.1+dfsg-1+b2 [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

provean (1.1.5+ds-5+b1 [arm64, loong64], 1.1.5+ds-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Protein Variation Effect Analyzer

pscan-chip (1.1-3+b4 [arm64], 1.1-3+b3 [amd64, armhf, i386, ppc64el, s390x], 1.1-3+b2 [loong64, 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+b4 [arm64], 1.2.2-4+b3 [amd64, armhf, i386, ppc64el, s390x], 1.2.2-4+b2 [riscv64], 1.2.2-4+b1 [loong64])

search for transcription factor binding sites

psfex (3.24.2-2+b1 [arm64], 3.24.2-2 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Point Spread Function model extractor

psychtoolbox-3-common (3.0.22.2+dfsg-3)

toolbox for vision research -- arch/interpreter independent part

psychtoolbox-3-lib (3.0.22.2+dfsg-3)

toolbox for vision research -- arch-specific parts

pullseq (1.0.2-5+b2 [arm64, loong64], 1.0.2-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Extract sequence from a fasta or fastq

purify (5.0.1-3)

Collection of routines for radio interferometric imaging

pycoqc (2.5.2+dfsg-5)

computes metrics and generates Interactive QC plots

pyensembl (2.6.9-1)

installs data from the Ensembl genome database

pyfastx (2.3.0-1+b1 [loong64], 2.3.0-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

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

pymca (5.9.4-2)

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

pymca-data (5.9.4-2)

Architecture independent data files for PyMca

pymoctool (0.5.2-3)

Python Multi-Order Coverage maps tool for Virtual Observatory

pymol (3.1.0+dfsg-1)

Molecular Graphics System

pymol-data (3.1.0+dfsg-1)

data files for PyMOL

pyomop (4.3.0-2)

OHSDI OMOP Common Data Model tools

pysatellites (2.7-4)

simulates the launching of satellites

python-drizzle-testdata (2.2.0-1)

Dithered image combination for Python (Test data)

python-pairix-examples (0.3.8-1)

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

python3-acres (0.5.0-3)

data-loading utility for Python

python3-adios4dolfinx (0.10.0.post0-4)

ADIOS2Wrappers for DOLFINx (Python 3)

python3-airr (1.5.1-2)

Data Representation Standard library for antibody and TCR sequences

python3-bioframe (0.8.0-2)

library to enable flexible, scalable operations on genomic interval dataframes

python3-bornagain (23.0-7)

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

python3-casadi (3.7.0+ds2-3)

Nonlinear optimization and algorithmic differentiation - Python bindings

python3-cif2cell (2.1.0+dfsg-3)

prepare CIF files for electronic structure calculations

python3-cykhash (2.0.0-4)

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

python3-cyvcf2 (0.32.0-1)

VCF parser based on htslib (Python 3)

python3-datacache (1.4.1-2)

helpers for transparently downloading datasets

python3-datalad-next (1.5.0-2)

DataLad extension for new features and improved user experience

python3-dcmstack (0.9+git20260610.ed4d27c-1)

DICOM to NIfTI conversion - python3 package

python3-deeptools (3.5.6+dfsg-1)

platform for exploring biological deep-sequencing data

python3-deeptoolsintervals (0.1.9-3+b13 [arm64], 0.1.9-3+b12 [amd64, armhf, i386, ppc64el, s390x], 0.1.9-3+b6 [riscv64], 0.1.9-3+b1 [loong64])

handlig GTF-like sequence-associated interal-annotation

python3-dnapilib (1.1-3)

adapter prediction for small RNA sequencing - library

python3-einops (0.8.1-1.1)

Flexible and powerful tensor operations for readable code

python3-faiss (1.13.2-1+b1)

Python 3 module for efficient similarity search and clustering of dense vectors

python3-ffcv (1.0.0+git20240506.3a12966-1)

Fast Forward Computer Vision (and other ML workloads)

python3-geneimpacts (0.3.7-5)

wraps command line tools to assess variants in gene sequences

python3-gfapy (1.2.3+dfsg-3+b1 [loong64], 1.2.3+dfsg-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

flexible and extensible software library for handling sequence graphs

python3-gffutils (0.13-5)

Work with GFF and GTF files in a flexible database framework

python3-gtfparse (1.3.0+ds-3)

parser for gene transfer format (aka GFF2)

python3-harmonypy (0.0.10-1)

is a data integration algorithm

python3-ihm (2.7-1+b1 [loong64], 2.7-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

handles mmCIF protein structural data

python3-jupyter-sphinx (0.5.3-3)

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-moltemplate (2.22.5-1)

text-based molecule builder for LAMMPS

python3-mpiplus (0.0.2+ds-1)

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

python3-nanostat (1.4.0-4)

statistics on long biological sequences

python3-navarp (1.6.0-4)

Navigation tool for ARPES data (Python 3)

python3-noise (1.2.3-4+b9 [arm64], 1.2.3-4+b8 [amd64, armhf, i386, ppc64el, s390x], 1.2.3-4+b6 [riscv64], 1.2.3-4+b1 [loong64])

Perlin noise for image generation

python3-onnx (1.20.0-5)

Open Neural Network Exchange (ONNX) (Python)

python3-parmed (4.3.1+dfsg-1)

parameter and topology file editor and molecular mechanical simulator

python3-pdbtools (2.6.0-1)

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

python3-peptidebuilder (1.1.0-3)

generate atomic oligopeptide 3D structure from sequence

python3-pomegranate (1.1.0-1)

Fast, flexible and easy to use probabilistic modelling

python3-prodigy (2.4.0-2)

Protein Binding Affinity Prediction (Python 3)

python3-propka (3.5.1-3)

heuristic pKa calculations with ligands (Python 3)

python3-py2bit (0.3.3-1+b2)

access to 2bit files

python3-pyaml-env (1.2.1-2)

Python3 YAML configuration with environment variables parsing

python3-pybel (0.15.5-4)

Biological Expression Language

python3-pybigwig (0.3.25+dfsg-1+b1 [loong64], 0.3.25+dfsg-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Python 3 module for quick access to bigBed and bigWig files

python3-pyimagetool (1.0-2)

Image Tool for multidimensional analysis (Python 3)

python3-pynlpl (1.2.9-3)

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

python3-pynndescent (0.6.0-1)

nearest neighbor descent for approximate nearest neighbors

python3-pyvista (0.46.5-8)

Python3 high-level API to the Visualization Toolkit (VTK)

python3-pyxrd (0.8.4-6)

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

python3-seqcluster (1.2.9+ds-7) [contrib]

analysis of small RNA in NGS data

python3-sercol (0.0+git20250731-2)

openvax immunoinformatics pipeline's helper classes

python3-skorch (1.1.0-1)

scikit-learn compatible neural network library that wraps PyTorch

python3-symfc (1.6.1-2)

Generate symmetrized force constants (Python 3)

python3-tinyalign (0.2.2-2)

numerical representation of differences between strings

python3-torch-cluster (1.6.3-2+b2 [arm64], 1.6.3-2+b1 [amd64, ppc64el, riscv64, s390x])

PyTorch extension library of optimized graph cluster algorithms (Python 3)

python3-torch-geometric (2.8.0-1)

Graph Neural Network Library for PyTorch

python3-torch-ignite (0.5.1-1)

High-level library to help with training and evaluating in PyTorch

python3-torch-scatter (2.1.2-4+b2 [arm64], 2.1.2-4+b1 [amd64, ppc64el, riscv64, s390x])

PyTorch Extension Library of Optimized Scatter Operations

python3-torch-sparse (0.6.18-3+b2 [arm64], 0.6.18-3+b1 [amd64, ppc64el, riscv64, s390x])

PyTorch Extension Library of Optimized Autograd Sparse Matrix Operations

python3-torchaudio (2.11.0-1)

Data manipulation and transformation for audio signal processing

python3-torchvision (0.27.0-3)

Datasets, Transforms and Models specific to Computer Vision

python3-truncnorm (0.0.2-3)

Moments for truncated multivariate normal distributions for Python

python3-weblogo (3.9.0-1)

sequence logo generator

python3-xeus-python-shell (0.18.1+~0.6.6-1)

Native jupyter kernel for python (python library)

python3-xraydb (4.5.3-2)

X-ray Reference Data (Python 3)

python3-xrt (1:2.21.75+dfsg-9)

Xilinx Runtime (XRT) - Python bindings

pyzo (4.15.0-3)

interactive editor for scientific Python

q2templates (2024.5.0+ds-4)

Design template package for QIIME 2 Plugins

qcat (1.1.0-9)

demultiplexing Oxford Nanopore reads from FASTQ files

qcat-examples (1.1.0-9)

demultiplexing Oxford Nanopore reads from FASTQ files (examples)

qemu-web-desktop (26.04.04+ds1-1)

Remote desktop service with virtual machines in a browser (DARTS).

qfits-tools (6.2.0-9+b2)

FITS manipulation tools

qfitsview (4.3+dfsg-1+b1 [arm64, loong64], 4.3+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

FITS file viewer based on DPUSER

qgis (3.44.11+dfsg-1)

Geographic Information System (GIS)

qgis-api-doc (3.44.11+dfsg-1)

QGIS API documentation

qgis-common (3.44.11+dfsg-1)

QGIS - architecture-independent data

qgis-plugin-grass (3.44.11+dfsg-1)

GRASS plugin for QGIS

qgis-plugin-grass-common (3.44.11+dfsg-1)

GRASS plugin for QGIS - architecture-independent data

qgis-provider-grass (3.44.11+dfsg-1)

GRASS provider for QGIS

qgis-providers (3.44.11+dfsg-1)

collection of data providers to QGIS

qgis-providers-common (3.44.11+dfsg-1)

collection of data providers to QGIS - architecture-independent files

qgis-server (3.44.11+dfsg-1)

QGIS server providing various OGC services

qgis-server-bin (3.44.11+dfsg-1)

QGIS server providing various OGC services (executables)

qgis-server-common (3.44.11+dfsg-1)

QGIS server providing various OGC services (data)

qgis-server-landingpage (3.44.11+dfsg-1)

QGIS server providing various OGC services (landing page)

qgis-server-wcs (3.44.11+dfsg-1)

QGIS server providing various OGC services (WCS)

qgis-server-wfs (3.44.11+dfsg-1)

QGIS server providing various OGC services (WFS)

qgis-server-wfs3 (3.44.11+dfsg-1)

QGIS server providing various OGC services (WFS 3)

qgis-server-wms (3.44.11+dfsg-1)

QGIS server providing various OGC services (WMS)

qgis-server-wmts (3.44.11+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 (1.20.3-1)

GPS mapping (GeoTiff and vector) and GPSr management

qmc (0.94-4.1+b2 [arm64], 0.94-4.1+b1 [loong64, riscv64], 0.94-4.1 [amd64, armhf, i386, ppc64el, s390x])

Quine McClusky Simplification Tool

qrisk2 (0.1.20150729-8)

cardiovascular disease risk calculator

qthid-fcd-controller (4.1-6+b4 [arm64], 4.1-6+b2 [amd64, armhf, i386, ppc64el, riscv64, s390x], 4.1-6+b1 [loong64])

Funcube Dongle controller

qtltools (1.3.1+dfsg-4+b5 [arm64], 1.3.1+dfsg-4+b4 [amd64, armhf, i386, ppc64el, riscv64, s390x], 1.3.1+dfsg-4+b1 [loong64])

Tool set for molecular QTL discovery and analysis

qttinysa (1.2.2-3)

QT Gui for a tiny SA Spectrum Analyser

quantum-espresso (6.7-4+b1 [arm64], 6.7-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Electronic-Structure and Ab-Initio Molecular Dynamics Suite

quantum-espresso-data (6.7-4)

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

quantum-espresso-data

virtual package provided by quantum-espresso-data-sssp

quantum-espresso-data-sssp (1.3.0-3)

Standard solid-state pseudopotentials (SSSP) library

quicktree (2.5-6+b2 [arm64], 2.5-6+b1 [loong64, riscv64], 2.5-6 [amd64, armhf, i386, ppc64el, s390x])

Neighbor-Joining algorithm for phylogenies

quorum (1.1.2-2+b2 [arm64, ppc64el, riscv64], 1.1.2-2+b1 [loong64], 1.1.2-2 [amd64])

QUality Optimized Reads of genomic sequences

qutemol (0.4.1~cvs20081111-15+b7 [arm64], 0.4.1~cvs20081111-15+b6 [riscv64], 0.4.1~cvs20081111-15+b5 [armhf, i386], 0.4.1~cvs20081111-15+b4 [amd64, ppc64el, s390x], 0.4.1~cvs20081111-15+b1 [loong64])

interactive visualization of macromolecules

racon (1.5.0-4+b1 [arm64, loong64], 1.5.0-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

radiant (2.8.1+dfsg-3)

explore hierarchical metagenomic data with zoomable pie charts

ragout (2.3-6)

Reference-Assisted Genome Ordering UTility

ragout-examples (2.3-6)

Reference-Assisted Genome Ordering UTility (example data)

rambo-k (1.21+dfsg-6)

Read Assignment Method Based On K-mers

rampler (2.1.1-1+b2 [arm64], 2.1.1-1+b1 [loong64, riscv64], 2.1.1-1 [amd64, armhf, i386, ppc64el, s390x])

module for sampling genomic sequences

rapmap (0.15.0+dfsg-5+b1)

rapid sensitive and accurate DNA read mapping via quasi-mapping

rapmap-dev (0.15.0+dfsg-5)

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

rapmap-example-data (0.15.0+dfsg-5)

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

raster3d (3.0-8-3)

tools for generating images of proteins or other molecules

rate4site (3.0.0-8+b2 [arm64], 3.0.0-8+b1 [loong64, riscv64], 3.0.0-8 [amd64, armhf, i386, ppc64el, s390x])

detector of conserved amino-acid sites

rawtran (1.1-1+b7 [arm64], 1.1-1+b5 [amd64, armhf, i386], 1.1-1+b4 [ppc64el, s390x], 1.1-1+b2 [riscv64], 1.1-1+b1 [loong64])

RAW photo to FITS converter

raxml (8.2.13+dfsg-3+b1)

Randomized Axelerated Maximum Likelihood of phylogenetic trees

ray (2.3.1-9+b1 [arm64], 2.3.1-9 [amd64, armhf, i386, ppc64el, riscv64, s390x])

de novo genome assemblies of next-gen sequencing data

ray-extra (2.3.1-9)

Scripts and XSL sheets for post-processing for ray

rdf2rml (0~20250711+dfsg-1)

convert RDF data to either R2RML script or PlantUML diagram

rdkit-data (202503.6-4)

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

rdp-classifier (2.10.2-8)

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

readseq (1-16+b2 [loong64], 1-16+b1 [arm64], 1-16 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Conversion between sequence formats

readucks (0.0.3-8)

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

reapr (1.0.18+dfsg-7+b2 [arm64], 1.0.18+dfsg-7+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

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

repeatmasker-recon (1.08-8+b3 [arm64], 1.08-8+b1 [loong64], 1.08-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

finds repeat families from biological sequences

reprof (1.0.1-10)

protein secondary structure and accessibility predictor

resfinder (4.4.2-3)

identify acquired antimicrobial resistance genes

resfinder-db (0.0+git20220524.fa32d9a-2)

ResFinder database is a curated database of acquired resistance genes

resfinder-example (4.4.2-3)

identify acquired antimicrobial resistance genes (example data)

rna-star (2.7.11b+dfsg-2+b4 [arm64], 2.7.11b+dfsg-2+b3 [amd64, ppc64el, riscv64], 2.7.11b+dfsg-2+b1 [loong64])

ultrafast universal RNA-seq aligner

rnahybrid (2.1.2-8+b2 [arm64, riscv64], 2.1.2-8+b1 [loong64], 2.1.2-8 [amd64, armhf, i386, 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+b3 [arm64], 1.2.1-2+b2 [amd64, armhf, i386, ppc64el, riscv64], 1.2.1-2+b1 [loong64])

NASA Chemical Equilibrium, wrapped in Python

roguenarok (1.0.1-3.1+b1 [arm64, loong64], 1.0.1-3.1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

versatile and scalable algorithm for rogue taxon identification

routine-update (0.2.6)

routine updater for a Debian source package

rsem (1.3.3+dfsg-4)

RNA-Seq by Expectation-Maximization

rtax (0.984-8)

Classification of sequence reads of 16S ribosomal RNA gene

ruby-rgfa (1.3.1+dfsg-3)

parse, edit and write GFA format graphs in Ruby

rudof (0.3.3+ds-1)

RDF data shape processing - CLI tool

runcircos-gui (0.0+git20200528.82dda8c-1+b3 [arm64], 0.0+git20200528.82dda8c-1+b2 [riscv64], 0.0+git20200528.82dda8c-1+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

GUI tool to run circos

sac2mseed (1.13+ds1-2)

Convert SAC waveform data to MiniSEED

saga (9.9.3+dfsg-2+b1)

System for Automated Geoscientific Analyses

saga-common (9.9.3+dfsg-2)

SAGA GIS architecture independent files

saint (2.5.0+dfsg-5+b1 [loong64], 2.5.0+dfsg-5 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Significance Analysis of INTeractome

salmid (0.1.23-5)

rapid Kmer based Salmonella identifier from sequence data

salmon (1.10.3+ds1-3+b1)

wicked-fast transcript quantification from RNA-seq data

samblaster (0.1.26-4+b2 [arm64], 0.1.26-4+b1 [loong64, riscv64], 0.1.26-4 [amd64, armhf, i386, ppc64el, s390x])

marks duplicates, extracts discordant/split reads

samclip (0.4.0-4)

filter SAM file for soft and hard clipped alignments

samtools (1.22.1-1+b1 [arm64, loong64], 1.22.1-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

processing sequence alignments in SAM, BAM and CRAM formats

samtools-test (1.22.1-1)

test files for the samtools package

saods9 (8.7+repack-1)

Image display tool for astronomy

saoxmlrpc (8.7+repack-1)

Tcl XML-RPC implementation from SAO

sasview (6.1.3-2)

Small Angle Scattering Analysis suite

sat4j (2.3.6-1)

Efficient library of SAT solvers in Java

savi (1.6.0-1+b3 [arm64], 1.6.0-1+b2 [riscv64], 1.6.0-1+b1 [loong64], 1.6.0-1 [amd64, armhf, i386, ppc64el, s390x])

satellite constellation visualisation

savvy-util (2.1.0-4+b1 [arm64, loong64], 2.1.0-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

conversion tool for SAV file format

sbmltoolbox (4.1.0-5.1)

libsbml toolbox for octave and matlab

scamp (2.15.0-1)

Compute astrometric and photometric solutions

science-config (1.15)

Debian Science Project config package

science-dataacquisition-dev (1.15)

Debian Science data acquisition development packages

science-electronics (1.15)

Debian Science Electronics transitional package

science-engineering-dev (1.15)

Debian Science Engineering-dev packages

science-highenergy-physics (1.15)

Debian Science High Energy Physics packages

science-highenergy-physics-dev (1.15)

Debian Science High Energy Physics development packages

science-machine-learning (1.15)

Debian Science Machine Learning packages

science-mathematics-dev (1.15)

Debian Science Mathematics-dev packages

science-meteorology-dev (1.15)

Debian Science Meteorology-dev packages

science-nanoscale-physics (1.15)

Debian Science Nanoscale Physics packages

science-nanoscale-physics-dev (1.15)

Debian Science Nanoscale Physics development packages

science-neuroscience-cognitive (1.15)

Debian Science packages for Cognitive Neuroscience

science-neuroscience-modeling (1.15)

Debian Science packages for modeling of neural systems

science-physics-dev (1.15)

Debian Science Physics-dev packages

science-robotics-dev (1.15)

Debian Robotics development packages

science-tasks (1.15)

Debian Science tasks for tasksel

science-viewing-dev (1.15)

Debian Science development of visualisation applications

scrappie (1.4.2-9+b2 [arm64], 1.4.2-9+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

basecaller for Nanopore sequencer

scrm (1.7.4-2+b1 [arm64, loong64], 1.7.4-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

simulator of evolution of genetic sequences

sctk (2.4.12+dfsg-1.1+b1 [arm64, loong64], 2.4.12+dfsg-1.1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

speech recognition scoring toolkit

scythe (0.994+git20141017.20d3cff-5+b2 [arm64], 0.994+git20141017.20d3cff-5+b1 [loong64], 0.994+git20141017.20d3cff-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Bayesian adaptor trimmer for sequencing reads

sdml (0.3.2+20250310-7+b1)

CLI tool for Simple Domain Modeling Language (SDML)

seaview (1:5.1+20251106-1+b1 [loong64], 1:5.1+20251106-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Multiplatform interface for sequence alignment and phylogeny

secrecy (0.0.5+ds-4+b3)

tool to handle libsecrecy keys and encrypted files

seer (1.1.4-9)

genomic sequence element (kmer) enrichment analysis

segemehl (0.3.4-5+b3 [arm64], 0.3.4-5+b2 [riscv64], 0.3.4-5+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

short read mapping with gaps

sentencepiece (0.2.1-2)

Unsupervised text tokenizer and detokenizer

seq-gen (1.3.5-2) [non-free]

simulate the evolution of nucleotide or amino acid sequences

seqan-apps (2.5.2-1+b1 [loong64], 2.5.2-1 [amd64, arm64, ppc64el, riscv64, s390x])

C++ library for the analysis of biological sequences

seqan-needle (1.0.3+ds-1+b1 [arm64, loong64], 1.0.3+ds-1 [amd64, ppc64el, riscv64])

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

seqan-raptor (3.0.1+ds-12)

pre-filter for querying very large collections of nucleotide sequences

seqan-raptor-doc (3.0.1+ds-12)

HTML & PDF documentation for seqan-raptor and its APIs

seqcluster (1.2.9+ds-7) [contrib]

analysis of small RNA in NGS data

seqkit (2.10.1+ds-1+b2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x], 2.10.1+ds-1+b1 [loong64])

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

seqkit-examples (2.10.1+ds-1)

examples for seqkit: toolkit for FASTA/Q file manipulation

seqmagick (0.8.6-4)

imagemagick-like frontend to Biopython SeqIO

seqprep (1.3.2-10+b1 [arm64, loong64], 1.3.2-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

seqprep-data (1.3.2-10)

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+b2 [arm64], 1.4-2+b1 [loong64, riscv64], 1.4-2 [amd64, armhf, i386, ppc64el, s390x])

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

seriation (1.0-1+b1 [arm64, loong64], 1.0-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

finds a suitable linear order for a set of objects

seriation-data (1.0-1)

test data for seriation

sga (0.10.15-7+b3 [armhf, i386, ppc64el, riscv64], 0.10.15-7+b2 [amd64, arm64, loong64])

de novo genome assembler that uses string graphs

shapeit4 (4.2.2+dfsg-1+b6 [arm64], 4.2.2+dfsg-1+b4 [amd64, armhf, i386, ppc64el, riscv64, s390x], 4.2.2+dfsg-1+b1 [loong64])

fast and accurate method for estimation of haplotypes (phasing)

shasta (0.14.0-3)

nanopore whole genome assembly (binaries and scripts)

shovill (1.1.0-11)

Assemble bacterial isolate genomes from Illumina paired-end reads

shovill-examples (1.1.0-11)

Test Data for shovill

sibelia (3.0.7+dfsg-6+b2 [loong64], 3.0.7+dfsg-6 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

comparative genomics tool

sibelia-examples (3.0.7+dfsg-6)

comparative genomics tool (example data)

sibsim4 (0.20-5+b2 [arm64], 0.20-5+b1 [loong64, riscv64], 0.20-5 [amd64, armhf, i386, ppc64el, s390x])

align expressed RNA sequences on a DNA template

sickle (1.33+git20150314.f3d6ae3-2+b2 [arm64], 1.33+git20150314.f3d6ae3-2+b1 [loong64, riscv64], 1.33+git20150314.f3d6ae3-2 [amd64, armhf, i386, ppc64el, s390x])

windowed adaptive trimming tool for FASTQ files using quality

sideretro (1.1.6-3)

pipeline for detecting Somatic Insertion of DE novo RETROcopies

sightcalibrator (25.2.0-2+b1)

Camera calibration software

sightviewer (25.2.0-2+b1)

DICOM viewer

sigma-align (1.1.3-9+b2 [arm64], 1.1.3-9+b1 [armhf, loong64], 1.1.3-9 [amd64, i386, ppc64el, riscv64, s390x])

Simple greedy multiple alignment of non-coding DNA sequences

sigviewer (0.6.4-3+b3 [arm64], 0.6.4-3+b2 [armhf, riscv64], 0.6.4-3+b1 [amd64, i386, ppc64el, s390x], 0.6.4-3 [loong64])

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

sim4 (0.0.20121010-9+b1 [arm64, loong64], 0.0.20121010-9 [amd64, armhf, i386, ppc64el, riscv64, s390x])

tool for aligning cDNA and genomic DNA

sim4db (0~20150903+r2013-10+b2)

batch spliced alignment of cDNA sequences to a target genome

simka (1.5.3-10+b1 [arm64, loong64], 1.5.3-10 [amd64, ppc64el, riscv64])

comparative metagenomics method dedicated to NGS datasets

simkamin (1.5.3-10)

approximate comparative metagenomics method dedicated to NGS datasets

simrisc (16.06.00-1+b1 [loong64], 16.06.00-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

simulation model for breast/lung cancer risk

siril (1.4.2-1+b1)

astronomical image processing tool

siril-common (1.4.2-1)

architecture-independent files for siril

ska (1.0+dfsg-6+b1 [loong64], 1.0+dfsg-6 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Split Kmer Analysis

skesa (2.4.0-8+b1)

strategic Kmer extension for scrupulous assemblies

skewer (0.2.2-6+b3 [arm64], 0.2.2-6+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

post-processing of high-throughput DNA sequence reads

skycat (3.1.2+starlink1~b+dfsg-10+b2 [loong64], 3.1.2+starlink1~b+dfsg-10+b1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Image visualization and access to catalogs and data for astronomy

slang-xfig (0.2.0~.138-3)

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

smalt (0.7.6-13+b2 [arm64], 0.7.6-13+b1 [loong64], 0.7.6-13 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Sequence Mapping and Alignment Tool

smalt-examples (0.7.6-13)

Sequence Mapping and Alignment Tool (examples)

smiles-scripts (0.4.0+dfsg-3)

command line tools to handle SMILES descriptors

smithwaterman (0.0+git20160702.2610e25-12+b3)

determine similar regions between two strings or genomic sequences

snakemake (7.32.4-11)

pythonic workflow management system

snap (2013-11-29-11+b3 [arm64], 2013-11-29-11+b2 [riscv64], 2013-11-29-11+b1 [loong64], 2013-11-29-11 [amd64, armhf, i386, ppc64el, s390x])

location of genes from DNA sequence with hidden markov model

snap-aligner (2.0.5+dfsg-1+b1 [arm64, loong64], 2.0.5+dfsg-1 [amd64, ppc64el, riscv64])

Scalable Nucleotide Alignment Program

snaphu (2.0.7-2) [non-free]

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

sniffles (2.6.0-1)

structural variation caller using third-generation sequencing

snp-sites (2.5.1-2+b3)

Binary code for the package snp-sites

snpomatic (1.0-7+b2 [arm64], 1.0-7+b1 [loong64], 1.0-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast, stringent short-read mapping software

soapaligner (2.20-6)

aligner of short reads of next generation sequencers

soapdenovo (1.05-7)

short-read assembly method to build de novo draft assembly

soapdenovo2 (242+dfsg-5)

short-read assembly method to build de novo draft assembly

soapsnp (1.03-5+b2 [arm64], 1.03-5+b1 [loong64, riscv64], 1.03-5 [amd64, armhf, i386, 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 (4.3.7-3+b1)

tool for filtering, mapping and OTU-picking NGS reads

source-extractor (2.28.2+ds-1+b1 [arm64, loong64], 2.28.2+ds-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Source extractor for astronomical images

sp800-90b-entropy-assessment (1.1.8-3+b1 [arm64, loong64], 1.1.8-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Estimating the quality of a source of entropy

spaced (1.2.0-201605+dfsg-4+b2 [arm64], 1.2.0-201605+dfsg-4+b1 [loong64], 1.2.0-201605+dfsg-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

alignment-free sequence comparison using spaced words

spades (4.0.0+really3.15.5+dfsg-3)

genome assembler for single-cell and isolates data sets

spaln (3.0.7+dfsg-1+b1 [arm64, loong64], 3.0.7+dfsg-1 [amd64, ppc64el, riscv64, s390x])

splicing-aware transcript-alignment to genomic DNA

spaln-data (3.0.7+dfsg-1)

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

spass (3.9-1.1+b1 [loong64, riscv64], 3.9-1.1 [amd64, arm64, armhf, i386, ppc64el, s390x])

automated theorem prover for first-order logic with equality

spatialite-bin (5.1.0a-2+b2 [arm64], 5.1.0a-2+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Geospatial extension for SQLite - tools

splash (3.12.0-1)

Visualisation tool for Smoothed Particle Hydrodynamics simulation

spoa (4.1.5-2)

SIMD partial order alignment tool

sprai (0.9.9.23+dfsg1-4)

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 (3.2.1+dfsg-6+b1)

utilities for the NCBI Sequence Read Archive

srst2 (0.2.0-14)

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 (1.1-16)

Smith-Waterman aligner based on libssw

stacks (2.68+dfsg-4)

pipeline for building loci from short-read DNA sequences

staden (2.0.0+b11-7+b1 [loong64], 2.0.0+b11-7 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

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

staden-common (2.0.0+b11-7)

Architecture independent files for Staden

staden-io-lib-examples (1.15.1-1)

programs for manipulating DNA sequencing files (usage examples)

staden-io-lib-utils (1.15.1-1)

programs for manipulating DNA sequencing files

stardata-common (0.9+b1 [loong64], 0.9 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Common framework to manage astronomy packages

starpu-examples (1.4.10+dfsg-2+b3)

Task scheduler for heterogeneous multicore machines - exs

stellarium (26.1-1)

real-time photo-realistic sky generator

stellarium-data (26.1-1)

Stellarium data files

step (4:26.04.0-1)

interactive physical simulator for KDE

stiff (2.4.0-8+b1 [arm64, loong64], 2.4.0-8 [amd64, armhf, i386, ppc64el, riscv64, s390x])

convert scientific FITS images to the TIFF format

stilts (3.5.4-1)

Starlink Tables Infrastructure Library Tool Set

stimfit (0.16.11-3+b1 [amd64], 0.16.11-3 [arm64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Program for viewing and analyzing electrophysiological data

stringtie (3.0.3+ds-1+b1 [loong64], 3.0.3+ds-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

assemble short RNAseq reads to transcripts

subarch-select (0.2-1)

Select among binaries based upon x86 microarchitecture support

subread (2.0.8+dfsg-1+b1 [arm64, loong64], 2.0.8+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64])

toolkit for processing next-gen sequencing data

subread-data (2.0.8+dfsg-1)

data files for subread package

suitename (0.4.130509+git20210223.ebb1325-1+b2 [arm64], 0.4.130509+git20210223.ebb1325-1+b1 [loong64, riscv64], 0.4.130509+git20210223.ebb1325-1 [amd64, armhf, i386, ppc64el, s390x])

categorize each suite in an RNA backbone

sumaclust (1.0.36+ds-4+b1 [arm64, loong64], 1.0.36+ds-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast and exact clustering of genomic sequences

sumatra (1.0.36+ds-3+b1 [arm64, loong64], 1.0.36+ds-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast and exact comparison and clustering of sequences

sumo (1.25.0+dfsg1-1+b2)

Simulation of Urban MObility (SUMO)

supercell (2.1.1+~0.0~git20221028.d8eeb73-4)

structure generation for crystals with substitutions and partial occupancies

surankco (0.0.r5+dfsg-5)

Supervised Ranking of Contigs in de novo Assemblies

surpyvor (0.5-2)

modification of VCF files with SURVIVOR

survex (1.4.21-1+b1)

cave surveying and mapping software

survex-aven (1.4.21-1+b1)

sophisticated cave survey viewer for Survex

survivor (1.0.7-6+b1 [loong64], 1.0.7-6 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

tool set for simulating/evaluating SVs

svim (2.0.0-5)

Structural variant caller for long sequencing reads

swarm (3.1.6+dfsg-1+b1 [arm64], 3.1.6+dfsg-1 [amd64, ppc64el])

robust and fast clustering method for amplicon-based studies

swarp (2.41.5-3+b1 [arm64, loong64], 2.41.5-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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-7+b1 [arm64, loong64], 3.2.1+dfsg-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

assessment of SNPs for their evolutionary advantage

t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b2 [arm64], 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1+b1 [loong64, riscv64], 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 [amd64, armhf, i386, 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 (1.22.1+ds2-1+b2)

generic indexer for TAB-delimited genome position files

tandem-mass (1:201702011-1+b1 [amd64, loong64, riscv64], 1:201702011-1 [arm64, armhf, i386, ppc64el, s390x])

mass spectrometry software for protein identification

tantan (51-1+b1 [arm64, loong64], 51-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

low complexity and tandem repeat masker for biosequences

tclfitsy (8.7+repack-1)

Tcl FITS Extension

terraintool (1.19-2)

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

theli (3.1.4-2+b2 [arm64], 3.1.4-2+b1 [amd64, loong64, ppc64el, riscv64, s390x])

Astronomical image data reduction pipeline

therion (6.4.0-1)

Cave surveying - 2D and 3D drawing software

therion-viewer (6.4.0-1)

Cave surveying - 3D viewer for therion models

theseus (3.3.0-15)

superimpose macromolecules using maximum likelihood

theseus-examples (3.3.0-15)

superimpose macromolecules using maximum likelihood (examples)

thesias (3.1.1-4+b1 [loong64], 3.1.1-4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Testing Haplotype Effects In Association Studies

tiddit (3.6.1+dfsg-2+b2 [amd64, arm64, armhf, i386, ppc64el, riscv64], 3.6.1+dfsg-2+b1 [loong64])

structural variant calling

tigr-glimmer (3.02b-6+b3 [arm64], 3.02b-6+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

Gene detection in archea and bacteria

timbl (6.10-3+b3)

Tilburg Memory Based Learner

timblserver (1.19-2+b2)

Server extensions for Timbl

tiny-dnn (1.0.0a3+ds-6)

header only deep learning framework in C++

tippecanoe (2.53.0-1+b2 [arm64], 2.53.0-1+b1 [loong64], 2.53.0-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

build vector tilesets from large collections of GeoJSON features

tksao (8.7+repack-1)

Tk widgets for astronomical imaging and data visualization

tm-align (20190822+dfsg-3+b1 [arm64, loong64], 20190822+dfsg-3 [amd64, armhf, i386, ppc64el, riscv64, s390x])

structural alignment of proteins

tombo (1.5.1-9)

identification of modified nucleotides from raw nanopore sequencing data

tophat-recondition (1.4-3)

post-processor for TopHat unmapped reads

topparser (1.3-4)

Conversion utility from pockettopo to therion, for cave surveying

toppic (1.8.0+repack1-3)

Top-down proteoform identification and characterization (programs)

toppic-common (1.8.0+repack1-3)

Top-down proteoform identification and characterization (common data)

toppred (1.10-10+b2 [arm64], 1.10-10+b1 [loong64, riscv64], 1.10-10 [amd64, armhf, i386, ppc64el, s390x])

transmembrane topology prediction

tortoize (2.0.16-2)

Application to calculate ramachandran z-scores

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-4+b1 [arm64, loong64], 3.0.6~beta+dfsg-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

interpretation of DNA Sanger sequencing data

transdecoder (6.0.0-3)

find coding regions within RNA transcript sequences

transfuse (0.7.6-2)

Runs formatted documents through transformations/translation

transrate-tools (1.0.0-7+b1 [arm64, loong64], 1.0.0-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

helper for transrate

transtermhp (2.09-5+b3 [arm64], 2.09-5+b2 [loong64, riscv64], 2.09-5 [amd64, armhf, i386, ppc64el, s390x])

find rho-independent transcription terminators in bacterial genomes

travis (220729-1+b2 [arm64], 220729-1+b1 [loong64, riscv64], 220729-1 [amd64, armhf, i386, ppc64el, s390x])

trajectory analyzer and visualizer

tree-ppuzzle (5.3~rc16+dfsg-14+b1 [arm64], 5.3~rc16+dfsg-14 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Parallelized reconstruction of phylogenetic trees by maximum likelihood

tree-puzzle (5.3~rc16+dfsg-14+b1 [arm64], 5.3~rc16+dfsg-14 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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+b6 [arm64], 0.5.1+git20100823.7e4d0e9-4+b4 [amd64, armhf, i386, ppc64el, s390x], 0.5.1+git20100823.7e4d0e9-4+b3 [riscv64], 0.5.1+git20100823.7e4d0e9-4+b1 [loong64])

Displays and prints phylogenetic trees

trf (4.09.1-6+b2 [arm64], 4.09.1-6+b1 [loong64, riscv64], 4.09.1-6 [amd64, armhf, i386, 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 (1.6-8) [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-5+b1 [arm64, loong64], 0.96+dfsg-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

toolkit to carry out genetic association for multi-category phenotypes

trnascan-se (2.0.12+ds-2) [non-free]

detection of transfer RNA genes in genomic sequence

trnascan-se-common (2.0.12+ds-2) [non-free]

detection of transfer RNA genes in genomic sequence (common files)

tunnelx (20190701-1)

Cave Survey drawing software

twms (0.07z+git20201202+bb7c3f8-2.1)

tiny web map service

twopaco (1.0.0+dfsg-2+b1 [arm64], 1.0.0+dfsg-2 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

build the compacted de Bruijn graph from many complete genomes

ubertooth (2018.12.R1-6)

2.4 GHz wireless development platform for Bluetooth experimentation

ubertooth-firmware (2018.12.R1-6)

Firmware for Ubertooth

ubertooth-firmware-source (2018.12.R1-6)

Source code for the Ubertooth firmware

uc-echo (1.12-19+b3 [arm64], 1.12-19+b1 [loong64], 1.12-19 [amd64, armhf, i386, ppc64el, riscv64, s390x])

error correction algorithm designed for short-reads from NGS

ucc-utils (1.7.0~rc1-1)

Utilities for the UCC Collectives library

ucto (0.35-2+b4)

Unicode Tokenizer

uctodata (0.11-2)

Data files for Ucto

ucx-utils (1.20.1-1)

Utilities for the UCX messaging library

ugene (52.1+dfsg-1+b1 [arm64], 52.1+dfsg-1 [amd64])

integrated bioinformatics toolkit

ugene-data (52.1+dfsg-1)

required data for UGENE - integrated bioinformatics toolkit

uhd-doc (4.9.0.1-1.3)

universal hardware driver for Ettus Research products - doc

uhd-host (4.9.0.1-1.3)

universal hardware driver for Ettus Research products - host apps

uncalled (2.3+ds-3+b4 [amd64, arm64], 2.3+ds-3+b3 [armhf, i386, ppc64el, riscv64, s390x], 2.3+ds-3+b1 [loong64])

Utility for Nanopore Current Alignment to Large Expanses of DNA

unifrac-tools (1.4-3+b5)

high-performance phylogenetic diversity calculations (binaries)

unihedron-device-manager (1.0.0.352+dfsg-2)

Unihedron Device manager (UDM)

unikmer (0.20.0-2+b1 [loong64], 0.20.0-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Toolkit for nucleic acid k-mer analysis

units-filter (4.2.1-1+b2 [arm64, riscv64], 4.2.1-1+b1 [amd64, armhf, i386, loong64, ppc64el, s390x])

Parser for expressions concerning physical values

units-master (4.2.1-1)

Powerful units converter with a GUI

v-sim (3.9.1-2)

Visualize atomic structures

v-sim-common (3.9.1-2)

Visualize atomic structures (support files)

v-sim-plugins (3.9.1-2)

Plugins for V_Sim (a 3D visualization package)

varna (3-93+ds-7)

Visualization Applet for RNA

varscan (2.4.3+dfsg-5) [non-free]

variant detection in next-generation sequencing data

vcfanno (0.3.7+ds-1+b2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x], 0.3.7+ds-1+b1 [loong64])

annotate a VCF with other VCFs/BEDs/tabixed files

vcfanno-examples (0.3.7+ds-1)

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

vcftools (0.1.17-1+b1 [arm64, loong64], 0.1.17-1 [amd64, armhf, i386, 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+dfsg1-10+b1 [loong64], 1.2.10+dfsg1-10 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Nucleic acid sequence assembler for very short reads

velvet-example (1.2.10+dfsg1-10)

Example data for the Velvet sequence assembler

velvet-long (1.2.10+dfsg1-10+b1 [loong64], 1.2.10+dfsg1-10 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Nucleic acid sequence assembler for very short reads, long version

velvet-tests (1.2.10+dfsg1-10)

Test data for the Velvet sequence assembler

velvetoptimiser (2.2.6-5)

automatically optimise Velvet do novo assembly parameters

veryfasttree (4.0.5+dfsg-2+b1 [arm64, loong64], 4.0.5+dfsg-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Speeding up the estimation of phylogenetic trees from sequences

veusz (4.1-1)

2D and 3D scientific plotting application with graphical interface

vienna-rna (2.7.0+dfsg-2) [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 (3.7.3-1)

visual servoing library - dataset reference files

vitables (3.1.0-2)

graphical tool to browse and edit PyTables and HDF5 files

vmatch (2.3.1+git20240412.b3b8ac0+dfsg-2+b1 [loong64], 2.3.1+git20240412.b3b8ac0+dfsg-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

large scale sequence analysis software

voro++ (0.5+revert-to-0.4.6+dfsg1-1+b2 [arm64], 0.5+revert-to-0.4.6+dfsg1-1+b1 [loong64, riscv64], 0.5+revert-to-0.4.6+dfsg1-1 [amd64, armhf, i386, 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 (1.29.4415+ds-1+b1 [loong64], 1.29.4415+ds-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

Voronoi diagram-based tool to find atom contacts

votca (2026-3)

Molecular dynamics analysis - coarse-graining and charge transport

votca-data (2026-3)

VOTCA molecular dynamics analysis - basis sets and scripts

votca-tutorials (2026-3)

VOTCA molecular dynamics analysis - tutorials

vsearch (2.30.4-1+b1 [loong64, riscv64], 2.30.4-1 [amd64, arm64, ppc64el])

tool for processing metagenomic sequences

vsearch-examples (2.30.4-1)

Test Data for vsearch tool for processing metagenomic sequences

vt (0.57721+ds-3+b3 [arm64], 0.57721+ds-3+b2 [armhf, riscv64], 0.57721+ds-3+b1 [amd64, i386, loong64, 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+b1 [arm64, loong64], 3.1.0+ds-10 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Maximally Localized Wannier Functions - executables

wannier90-data (3.1.0+ds-10)

Maximally Localized Wannier Functions - documentation and examples

wcslib-tools (8.5+ds-1)

Command line tools utilizing wcslib

wcstools (3.9.7-2+b2)

Handle the WCS of a FITS image

weightwatcher (1.12+dfsg-3+b2 [arm64, loong64], 1.12+dfsg-3+b1 [riscv64], 1.12+dfsg-3 [amd64, armhf, i386, ppc64el, s390x])

Combine maps and polygon data for astronomical image processing

weii (0.1.2-5)

read Wii balance board as a weight scale

weka (3.6.14-4)

Machine learning algorithms for data mining tasks

wham-align (0.1.5-8+b3 [arm64], 0.1.5-8+b1 [loong64, riscv64], 0.1.5-8 [amd64, armhf, i386, ppc64el, s390x])

Wisconsin's High-Throughput Alignment Method

wigeon (20101212+dfsg1-6)

reimplementation of the Pintail 16S DNA anomaly detection utility

wise (2.4.1-28)

comparison of biopolymers, like DNA and protein sequences

wsclean (3.7-1+b1)

Fast generic widefield interferometric imager

wtdbg2 (2.5-11)

de novo sequence assembler for long noisy reads

wtdbg2-examples (2.5-11)

Examples for wtdbg - de novo sequence assembler

wxastrocapture (1.8.1+git20140821.796e1a1+dfsg-2+b4 [amd64, arm64, armhf, i386, ppc64el, s390x], 1.8.1+git20140821.796e1a1+dfsg-2+b3 [riscv64], 1.8.1+git20140821.796e1a1+dfsg-2+b1 [loong64])

Windows linuX Astronomy Capture

x13as (1.1-b62-1) [non-free]

seasonal adjustment software for modeling time series

xbs (0-12+b1 [loong64], 0-12 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

3-d models and movies of molecules

xcas (1.9.0.93+dfsg2-4)

Computer Algebra System - console and graphical calculator

xcrysden (1.6.2-5+b1 [arm64, loong64], 1.6.2-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Crystalline and Molecular Structure Visualizer

xcrysden-data (1.6.2-5)

Crystalline and Molecular Structure Visualizer (Data Files)

xdrawchem (1:1.11.1-2+b1 [arm64, loong64], 1:1.11.1-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Chemical structures and reactions editor

xfoil (6.99.dfsg+1-3+b3 [arm64], 6.99.dfsg+1-3+b1 [amd64, armhf, i386, loong64, ppc64el, riscv64, s390x])

program for the design and analysis of subsonic airfoils

xgterm (2.2+dfsg-1+b1 [arm64], 2.2+dfsg-1 [amd64, armhf, i386, loong64, ppc64el, riscv64])

Terminal emulator to work with IRAF

ximtool (2.2+dfsg-1+b1 [arm64], 2.2+dfsg-1 [amd64, armhf, i386, loong64, ppc64el, riscv64])

Interactive image display program for the X Window System

xmakemol (5.16-12)

program for visualizing atomic and molecular systems

xmakemol-gl (5.16-12)

program for visualizing atomic and molecular systems (OpenGL)

xmds2 (3.1.0+dfsg2-13)

eXtensible Multi-Dimensional Simulator

xmpsolve (3.2.3-1+b2)

Multiprecision polynomial solver (graphical version)

xpa-tools (2.1.20-3+b2)

Tools for seamless communication between Unix programs

xplot (1.19-9.2+b1 [loong64], 1.19-9.2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

simple on-screen x-y column data plotter

xplot-xplot.org (0.90.7.1-5+b1 [arm64, loong64], 0.90.7.1-5 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast tool to graph and visualize lots of data

xpore (2.1-2)

Nanopore analysis of differential RNA modifications

xppaut (8.0+dfsg-1+b1 [arm64, loong64], 8.0+dfsg-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Phase Plane Plus Auto: Solves many kinds of equations

xpython (0.18.1+~0.6.6-1)

Native jupyter kernel for python (binary)

xtb (6.7.1-3+b1 [loong64], 6.7.1-3 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

semiempirical extended tight-binding program package

xyscan (4.68-1+b1 [arm64, loong64], 4.68-1 [amd64, armhf, i386, ppc64el, riscv64, s390x])

data thief for scientists

yaha (0.1.83-3+b2 [arm64], 0.1.83-3+b1 [loong64, riscv64], 0.1.83-3 [amd64, armhf, i386, 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 (1.0.0-6)

filter low quality Oxford Nanopore reads basecalled with Albacore

yanosim (0.1-8+b1 [loong64], 0.1-8 [amd64, arm64, armhf, i386, ppc64el, riscv64])

read simulator nanopore DRS datasets

yorick (2.2.04+dfsg1-17)

interpreted language and scientific graphics

yorick-av (0.0.6-2+b1 [loong64], 0.0.6-2 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

write movies from Yorick in various formats

yorick-cubeview (2.2-3)

3D FITS data viewer specialized in spectro-imaging

yorick-curses (0.1-7+b1 [arm64, loong64], 0.1-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

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

yorick-data (2.2.04+dfsg1-17)

interpreted library for the Yorick language

yorick-dev (2.2.04+dfsg1-17)

development files for the Yorick interpreted language

yorick-full (2.2.04+dfsg1+full+b1 [amd64, riscv64], 2.2.04+dfsg1+full [arm64, armhf, i386, ppc64el, s390x])

full installation of the Yorick interpreter and add-ons

yorick-gl (1.1+cvs20070922+dfsg-7+b1 [arm64, loong64], 1.1+cvs20070922+dfsg-7 [amd64, armhf, i386, ppc64el, riscv64, s390x])

OpenGL 3D graphics support for the Yorick language

yorick-gy (0.0.6-1+b1 [loong64], 0.0.6-1 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x])

GObject introspection and Gtk bindings for Yorick

yorick-gyoto (2.0.2-8)

General relativistic geodesic integration for the Yorick language

yorick-hdf5 (0.8.0-9+b3 [arm64], 0.8.0-9+b2 [amd64, armhf, i386, ppc64el, riscv64], 0.8.0-9+b1 [loong64, s390x])

Hierarchical Data Format 5 interface for the Yorick language

yorick-imutil (0.5.7-4+b1 [arm64, loong64], 0.5.7-4 [amd64, armhf, i386, ppc64el, riscv64, s390x])

fast image manipulation routines for the Yorick language

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

optical interferometry image reconstruction within Yorick

yorick-ml4 (0.6.0-6+b1 [arm64, loong64], 0.6.0-6 [amd64, armhf, i386, ppc64el, riscv64, s390x])

Matlab file format support for the Yorick language

yorick-mpeg (0.1-4+b2 [arm64], 0.1-4+b1 [loong64, riscv64], 0.1-4 [amd64, armhf, i386, ppc64el, s390x])

MPEG output support for the Yorick language

yorick-optimpack (1.3.2+dfsg+1.4.0-2+b1 [arm64, loong64], 1.3.2+dfsg+1.4.0-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

optimization of large scale problems for the Yorick language

yorick-soy (1.4.0-4+b1 [amd64, arm64, loong64], 1.4.0-4 [armhf, i386, ppc64el, riscv64, s390x])

sparse matrix operations for the Yorick language

yorick-svipc (0.16-7+b4 [amd64, arm64, armhf, i386, ppc64el, riscv64, s390x], 0.16-7+b1 [loong64])

interprocess communication (shared memory...) for Yorick

yorick-yeti (6.4.0-2+b1 [arm64], 6.4.0-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

utility plugin for the Yorick language

yorick-yeti-fftw (6.4.0-2+b1 [arm64], 6.4.0-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

FFT plugin for the Yorick language

yorick-yeti-regex (6.4.0-2+b1 [arm64], 6.4.0-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

POSIX regular expressions for the Yorick language

yorick-yeti-tiff (6.4.0-2+b1 [arm64], 6.4.0-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

TIFF image format input for the Yorick language

yorick-ygsl (1.2.1-2+b1 [arm64, loong64], 1.2.1-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

GSL special functions plugin for the Yorick language

yorick-ynfft (1.0.4-2+b1 [arm64, loong64], 1.0.4-2 [amd64, armhf, i386, ppc64el, riscv64, s390x])

nonequispaced fast Fourier transform for Yorick

yorick-yutils (1.5.2-2)

various utilities for the Yorick language

yorick-z (1.2.0+cvs20080115-7)

zlib, jpeg and png support for the Yorick language

z3 (4.13.3-1.1)

theorem prover from Microsoft Research

zegrapher (3.1.1-6)

plotting mathematical functions and sequences on the plane

zfp (1.0.1-4+b7)

Fixed-Rate Compressed Floating-Point Arrays - binary programs

zimpl (3.7.1+ds-1)

mathematical modeling language for optimization problems (binary)

ztex-bmp (20120314-3)

universal macro processor