Software Packages in "experimental", Subsection science

bali-phy (4.0~beta13+dfsg-1 [amd64, arm64, i386, m68k, ppc64, ppc64el, s390x], 4.0~beta2+dfsg-1 [armhf, ia64, mips64el])

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, sh4], 7.0.2+repack-1~exp1+b1 [hppa, i386, riscv64, sparc64, x32], 7.0.2+repack-1~exp1 [alpha, amd64, arm64, m68k, mips64el, ppc64, ppc64el, s390x])

General purpose Computational Fluid Dynamics (CFD) software

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

General purpose Computational Fluid Dynamics (CFD) software - includes

coinor-libcoinutils3v5 (2.11.11+ds-1~exp1)

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+b1 [riscv64], 36.3.8i.14-Nov-2020-2~0exp0simde [alpha, amd64, arm64, armel, armhf, hppa, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

tools for searching collections of biological sequences

fml-asm (0.1+git20190320.b499514-2~0exp+b1 [riscv64], 0.1+git20190320.b499514-2~0exp [alpha, amd64, arm64, armel, armhf, hppa, i386, ia64, m68k, mips64el, ppc64, ppc64el, s390x, sh4, sparc64, x32])

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

gazebo (11.10.2+dfsg-1+b1)

Open Source Robotics Simulator - Binaries

gazebo-common (11.10.2+dfsg-1)

Open Source Robotics Simulator - Shared files

gazebo-plugin-base (11.10.2+dfsg-1+b1)

Open Source Robotics Simulator - base plug-ins

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

Compression plugin for the HDF5 library using ZFP compression

hdf5-helpers (1.14.4.3+repack-1~exp3 [alpha, amd64, arm64, armel, armhf, i386, m68k, mips64el, ppc64el, riscv64, s390x, sh4, sparc64, x32], 1.14.3+repack1-1~exp3 [ia64, ppc64], 1.12.2+repack-1~exp1 [hppa])

HDF5 - Helper tools

hdf5-tools (1.14.4.3+repack-1~exp3 [alpha, amd64, arm64, armel, armhf, i386, m68k, mips64el, ppc64el, riscv64, s390x, sh4, sparc64, x32], 1.14.3+repack1-1~exp3 [ia64, ppc64], 1.12.2+repack-1~exp1 [hppa])

HDF5 - Runtime tools

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 (5:3.7.0-2+b1 [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 (5:3.7.0-2)

data files for KStars desktop planetarium

libhdf5-jni (1.14.4.3+repack-1~exp3 [alpha, amd64, arm64, armel, armhf, i386, m68k, mips64el, ppc64el, riscv64, s390x, sh4, sparc64, x32], 1.14.3+repack1-1~exp3 [ia64, ppc64])

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

libonnx-dev (1.16.1-1)

Open Neural Network Exchange (ONNX) (dev)

libonnx-testdata (1.16.1-1)

Open Neural Network Exchange (ONNX) (test data)

libonnx1t64 (1.16.1-1)

Open Neural Network Exchange (ONNX) (libs)

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

development files for prediction of orbits of earth satellites

libtorch-test (2.1.2+dfsg-1)

Tensors and Dynamic neural networks in Python (Test Binaries)

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~rc1-1~exp1)

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

openstructure (2.6.1-1~exp [amd64, mips64el], 2.6.0~rc-1~exp [sh4])

Open-Source Computational Structural Biology Framework

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

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

python3-onnx (1.16.1-1)

Open Neural Network Exchange (ONNX) (Python)

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

sasview (5.0.5-2)

Small Angle Scattering Analysis suite

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

basecaller for Nanopore sequencer

seqan-apps (2.5.0~rc2+dfsg-2)

C++ library for the analysis of biological sequences

sequitur-g2p (0+r1668.r3-1)

Grapheme to Phoneme conversion tool

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

SIMD partial order alignment tool

sra-toolkit (3.0.9+dfsg-6)

utilities for the NCBI Sequence Read Archive

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

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

vowpal-wabbit (8.6.1.dfsg1-1.1~exp1) [debports]

fast and scalable online machine learning algorithm

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