Källkodspaket i "experimental", Undersektion science

bali-phy (4.0~beta16 dfsg-1 [amd64, arm64, i386, m68k, mips64el, ppc64, ppc64el, riscv64, s390x, sparc64], 4.0~beta2 dfsg-1 [armhf, ia64])

Bayesian Inference of Alignment and Phylogeny

bwa (0.7.17-8~0exp) [debports]

Burrows-Wheeler Aligner

cgns-convert (4.2.0-1~exp1 [alpha, amd64, arm64, armel, armhf, ia64, m68k, mips64el, ppc64, ppc64el, riscv64, s390x, sh4, sparc64, x32], 4.1.2-1~exp1 [hppa, i386])

CFD General Notation System - Conversion tools

cnrun-tools (2.1.0-3 b2 [riscv64], 2.1.0-3 b1 [alpha, amd64, arm64, armel, armhf, hppa, i386, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32], 2.1.0-3 [ia64])

NeuroML-capable neuronal network simulator (tools)

cnvkit (0.9.10-3~0exp0)

Copy number variant detection from targeted DNA sequencing

code-saturne (7.0.2 repack-1~exp1 b2 [armel, armhf, m68k, sh4], 7.0.2 repack-1~exp1 b1 [hppa, i386, riscv64, sparc64, x32], 7.0.2 repack-1~exp1 [alpha, amd64, arm64, mips64el, ppc64, ppc64el, s390x])

General purpose Computational Fluid Dynamics (CFD) software

code-saturne-bin (7.0.2 repack-1~exp1 b2 [armel, armhf, m68k, sh4], 7.0.2 repack-1~exp1 b1 [hppa, i386, riscv64, sparc64, x32], 7.0.2 repack-1~exp1 [alpha, amd64, arm64, mips64el, ppc64, ppc64el, s390x])

General purpose Computational Fluid Dynamics (CFD) software - binaries

code-saturne-data (7.0.2 repack-1~exp1)

General purpose Computational Fluid Dynamics (CFD) software - data

code-saturne-doc (7.0.2 repack-1~exp1)

General purpose Computational Fluid Dynamics (CFD) software - Documentation

code-saturne-include (7.0.2 repack-1~exp1 b2 [armel, armhf, m68k, sh4], 7.0.2 repack-1~exp1 b1 [hppa, i386, riscv64, sparc64, x32], 7.0.2 repack-1~exp1 [alpha, amd64, arm64, mips64el, ppc64, ppc64el, s390x])

General purpose Computational Fluid Dynamics (CFD) software - includes

coinor-libcoinutils3v5 (2.11.11 ds-1~exp1) [debports]

COIN-OR collection of utility classes (shared libraries)

critterding (1.0-beta14 dfsg-2 b3 [amd64], 1.0-beta14 dfsg-2 b2 [arm64, armel, armhf, i386, ppc64el, s390x], 1.0-beta14 dfsg-2 b1 [mips64el, ppc64, x32], 1.0-beta14 dfsg-2 [alpha, hppa, m68k, sparc64])

Evolving Artificial Life

critterding-common (1.0-beta14 dfsg-2 b1)

Evolving Artificial Life - architecture-independent files

dcmtk (3.6.8~git20221024.b8950f9-3) [debports]

OFFIS DICOM toolkit command line utilities

ectrans-utils (1.2.0-1) [debports]

Spherical Harmonics Transforms library - utilities

examl (3.0.22-4~0exp) [debports]

Exascale Maximum Likelihood (ExaML) code for phylogenetic inference

fasta3 (36.3.8i.14-Nov-2020-2~0exp0simde) [debports]

tools for searching collections of biological sequences

flexbar (1:3.5.0-6)

flexible barcode and adapter removal for sequencing platforms

fml-asm (0.1 git20190320.b499514-2~0exp) [debports]

tool for assembling Illumina short reads in small regions

freebayes (1.3.7-1~exp b1 [amd64, arm64, ia64, m68k, mips64el, ppc64, ppc64el, sh4], 1.3.7-1~exp [armel, armhf, i386, riscv64, s390x, sparc64])

Bayesian haplotype-based polymorphism discovery and genotyping

freecad (1.0.0 dfsg-5~exp1)

Extensible Open Source CAx program

freecad-common (1.0.0 dfsg-5~exp1)

Extensible Open Source CAx program - common files

freecad-python3 (1.0.0 dfsg-5~exp1)

Extensible Open Source CAx program - Python 3 binaries

gromacs (2025.0~beta-1)

Molecular dynamics simulator, with building and analysis tools

gromacs-data (2025.0~beta-1)

GROMACS molecular dynamics sim, data and documentation

hdf5-filter-plugin-zfp-serial (1.1.0 git20230428-0 exp2) [debports]

Compression plugin for the HDF5 library using ZFP compression

hdf5-helpers (1.14.3 repack1-1~exp3 [ia64], 1.12.2 repack-1~exp1 [riscv64]) [debports]

HDF5 - Helper tools

hdf5-tools (1.14.3 repack1-1~exp3 [ia64], 1.12.2 repack-1~exp1 [riscv64]) [debports]

HDF5 - Runtime tools

hilive (2.0a-5)

realtime alignment of Illumina reads

hisat2 (2.2.1-5~0exp) [debports]

graph-based alignment of short nucleotide reads to many genomes

iraf (2.18.1~rc1-3~5)

Image Reduction and Analysis Facility

iraf-dev (2.18.1~rc1-3~5)

Image Reduction and Analysis Facility (development files)

iraf-noao (2.18.1~rc1-3~5)

IRAF NOAO data reduction package

iraf-noao-dev (2.18.1~rc1-3~5)

IRAF NOAO data reduction package (development files)

khmer (3.0.0~a3 dfsg-9~0exp b1)

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

khmer-common (3.0.0~a3 dfsg-9~0exp)

common files for the khmer project tools

kstars (5:3.7.4-2 [amd64, arm64, armel, armhf, i386, mips64el, ppc64, ppc64el, riscv64, s390x], 5:3.6.7-1 [alpha, sh4])

desktop planetarium, observation planning and telescope control

kstars-data (5:3.7.4-2)

data files for KStars desktop planetarium

lambda-align (1.0.3-7)

Local Aligner for Massive Biological DatA

libhdf5-jni (1.14.3 repack1-1~exp3 [ia64], 1.12.2 repack-1~exp1 [riscv64]) [debports]

native library used by libhdf5-java

liblinear-tools (2.43 dfsg-1 b1 [riscv64], 2.43 dfsg-1 [alpha, amd64, arm64, armel, armhf, hppa, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

Standalone applications for LIBLINEAR

libpluto-sat-code-dev (0.0~git20180301-1)

development files for prediction of orbits of earth satellites

lttoolbox-dev (3.7.1-2) [debports]

Development tools and library for lttoolbox

lua-cnrun (2.1.0-3 b2 [riscv64], 2.1.0-3 b1 [alpha, amd64, arm64, armel, armhf, hppa, i386, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32], 2.1.0-3 [ia64])

NeuroML-capable neuronal network simulator (Lua package)

m2m-aligner (1.2-2 b1 [riscv64], 1.2-2 [alpha, amd64, arm64, armel, armhf, hppa, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

many-to-many alignments for string transduction

minimap2 (2.24 dfsg-4~0exp b1) [debports]

versatile pairwise aligner for genomic and spliced nucleotide sequences

mmb (4.0.0 dfsg-3.1~exp1)

model the structure and dynamics of macromolecules

mmb-common (4.0.0 dfsg-3.1~exp1)

model the structure and dynamics of macromolecules (common files)

netcdf-bin (1:4.9.3~rc2-1~exp1 b1 [amd64, arm64, armel, armhf, i386, mips64el, ppc64, ppc64el, riscv64, s390x, sparc64], 1:4.9.3~rc2-1~exp1 [hppa, m68k, sh4], 1:4.9.3~rc1-1~exp1 [alpha, x32])

Programs for reading and writing NetCDF files

ngmlr (0.2.7 git20210816.a2a31fb dfsg-4~0exp0simde b1 [riscv64], 0.2.7 git20210816.a2a31fb dfsg-4~0exp0simde [alpha, amd64, arm64, armel, armhf, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

CoNvex Gap-cost alignMents for Long Reads

occt-draw (7.7.1 dfsg1-1~exp2) [debports]

Open CASCADE Technology command interpreter and graphical test system

opentelemetry-proto (1.5.0-1~exp1)

OpenTelemetry protocol specification and proto files

openturns-common (1.24-1)

generic tool to treat and quantify uncertainties (common files)

ovito (3.10.5~ds-1)

Scientific data visualization and analysis software for atomistic and molecular

phonetisaurus (0.7.8-6 b1 [alpha, amd64, arm64, armel, armhf, hppa, i386, m68k, mips64el, ppc64, ppc64el, s390x, sparc64, x32], 0.7.8-6 [sh4])

Grapheme to Phoneme conversion tool

pizzly (0.37.3 ds-10)

Identifies gene fusions in RNA sequencing data

plink2 (2.00~a3.5-220809 dfsg-2~0exp0simde) [debports]

whole-genome association analysis toolset

pluto-find-orb (0.0~git20180227-5)

orbit assessment from asteroid images

pluto-sat-code (0.0~git20180301-1)

prediction of orbits of earth satellites

porechop (0.2.4 dfsg-8)

adapter trimmer for Oxford Nanopore reads

pyfai (2024.09-1)

Fast Azimuthal Integration scripts

q2-phylogeny (2022.11.1-1)

QIIME 2 plugin for phylogeny

r-cran-alakazam (1.3.0-2~0exp0)

Immunoglobulin Clonal Lineage and Diversity Analysis

samtools (1.21-0 exp1)

processing sequence alignments in SAM, BAM and CRAM formats

samtools-test (1.21-0 exp1)

test files for the samtools package

sasview (6.0.0-2)

Small Angle Scattering Analysis suite

scrappie (1.4.2-9~0exp0simde b2 [armhf, riscv64], 1.4.2-9~0exp0simde b1 [amd64, arm64, i386, mips64el, ppc64, ppc64el, s390x, sparc64])

basecaller for Nanopore sequencer

seqan-apps (2.5.0~rc3 dfsg-1)

C library for the analysis of biological sequences

sequitur-g2p (0 r1668.r3-1) [debports]

Grapheme to Phoneme conversion tool

shasta (0.12.0-2)

nanopore whole genome assembly (binaries and scripts)

sibelia (3.0.7 dfsg-4)

comparative genomics tool

sibelia-examples (3.0.7 dfsg-4)

comparative genomics tool (example data)

spades (4.0.0 dfsg1-1)

genome assembler for single-cell and isolates data sets

spoa (4.0.8-2~0exp0simde) [debports]

SIMD partial order alignment tool

ssw-align (1.2.5-1 b1 [riscv64], 1.2.5-1 [alpha, amd64, arm64, armel, armhf, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

Smith-Waterman aligner based on libssw

staden (2.0.0 b11-5~rc1) [debports]

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

sump-logicanalyzer (0.8-1)

GUI controlling multiple logic analysers

tabix (1.21 ds-0 exp2)

generic indexer for TAB-delimited genome position files

tinysvm (0.09 dfsg-2 b1 [riscv64], 0.09 dfsg-2 [alpha, amd64, arm64, armel, armhf, hppa, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

SVM trainer and classifier toolkit

ucx-utils (1.18.0 ds~rc1-2 [arm64], 1.18.0 ds~rc1-1 [amd64, riscv64])

Utilities for the UCX messaging library

unicycler (0.5.1 dfsg-2)

hybrid assembly pipeline for bacterial genomes

unicycler-data (0.5.1 dfsg-2)

hybrid assembly pipeline for bacterial genomes (data package)

yamcha (0.33-2)

general purpose chunker annotator

yorick-optimpack (1.4.0~pre1 dfsg-1~exp0 b1 [riscv64], 1.4.0~pre1 dfsg-1~exp0 [alpha, amd64, arm64, armel, armhf, hppa, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

optimization of large scale problems for the Yorick language