Science

Note: For possibly more up to date selection of scientific applications, try checking the AUR 'science' category

Mathematics

Calculator

Console

bc — Arbitrary precision calculator language.

https://www.gnu.org/software/bc/ || bc

calc — Arbitrary precision console calculator.

http://www.isthe.com/chongo/tech/comp/calc/ || calc

clac — Command-line, stack-based calculator with postfix notation.

https://github.com/soveran/clac || clacAUR

kalker — Command-line calculator with math syntax that supports user-defined variables and functions, complex numbers, and estimation of derivatives and integrals.

https://github.com/PaddiM8/kalker || kalkerAUR

qalc — Command-line calculator and equation solver with fault-tolerant parsing, constant recognition and units.

https://qalculate.github.io/ || libqalculate

Graphical

Deepin Calculator — Easy to use calculator for Deepin desktop.

https://www.deepin.org/en/original/deepin-calculator/ || deepin-calculator

Extcalc — Qt-based scientific graphical calculator.

http://extcalc-linux.sourceforge.net/ || extcalcAUR

FOX Calculator — Simple desktop calculator.

http://fox-toolkit.org/ || fox

galculator — GTK-based scientific calculator.

http://galculator.mnim.org/ || galculator

Genius — Advanced calculator including a mathematical programming language.

https://www.jirka.org/genius.html || geniusAUR

GNOME Calculator — Scientific calculator included in the GNOME desktop.

https://wiki.gnome.org/Apps/Calculator || gnome-calculator

KAlgebra — Calculator and 3D plotter. Part of kde-education.

https://apps.kde.org/kalgebramobile/ || kalgebra

KCalc — Scientific calculator included in the KDE desktop.

https://apps.kde.org/kcalc/ || kcalc

Liri Calculator — Calculator for Liri.

https://github.com/lirios/calculator || liri-calculator

MATE Calc — Calculator for the MATE desktop environment.

https://mate-desktop.org/ || mate-calc

Qalculate! — Calculator and equation solver with fault-tolerant parsing, constant recognition and units.

https://qalculate.github.io/ || GTK: qalculate-gtk, Qt: qalculate-qt

SpeedCrunch — Fast, high precision and powerful cross-platform calculator.

https://speedcrunch.org || speedcrunch

xcalc — Scientific calculator for X with algebraic and reverse polish notation modes.

https://www.x.org/ || xorg-xcalc

Computer algebra system

AXIOM — FriCAS: derivative of the powerful AXIOM-CAS

https://fricas.sourceforge.net || fricasAUR

GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.

https://www.gap-system.org/ || gap

Maple — Famous commercial CAS. Often used in education.

https://www.maplesoft.com/products/maple/ ||

Mathics — A free CAS for symbolic mathematical computations which uses Python as its main language. It aims at achieving a Mathematica-compatible syntax and functions. It relies mostly on Sympy for most mathematical tasks and, optionally, Sage for more advanced functionality.

https://mathics.github.io/ || mathicsAUR

Mathomatic — General purpose Computer Algebra System written in C.

https://github.com/mfillpot/mathomatic || mathomatic

Maxima — Maple/Mathematica-like computer algebra system.

http://maxima.sourceforge.net/ || maxima

PARI/GP — Computer algebra system designed for fast computations in number theory.

https://pari.math.u-bordeaux.fr/ || pari

Singular — Computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.

https://www.singular.uni-kl.de/ || singular

wxMaxima — Graphical user interface for Maxima being a powerful computer algebra system.

https://andrejv.github.io/wxmaxima/ || wxmaximaAUR

Xcas — User interface to Giac, a free, basic computer algebra system.

https://www-fourier.ujf-grenoble.fr/~parisse/giac.html || giac

Visualization of networks/graphs

Graphia — Visualizes large graphs specified in various formats (including GML and GraphML) in 3D space in real time. See this issue on the Graphia Github for the Arch Linux package dependencies of Graphia.

https://graphia.app || not packaged? search in AUR

Graphviz — The established tool for displaying smallish graphs in 2D.

https://www.graphviz.org || graphviz

Scientific or technical computing

Cadabra — A field-theory motivated approach to computer algebra.

https://cadabra.science/ || cadabra2AUR

Cantor — Application that lets you use your favorite mathematical applications from within a nice KDE-integrated Worksheet Interface. Part of kde-education.

https://cantor.kde.org/ || cantor

EngLab — Cross-compile mathematical platform with a C like syntax.

http://englab.bugfest.net || englabAUR

FFTW — A Fast Fourier Transform library for computing discrete Fourier transforms. Used for a wide variety of numerical applications, which includes spectral methods.

https://www.fftw.org/ || fftw

FreeMat — Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.

https://freemat.sourceforge.net/ || freematAUR

GeoGebra — Dynamic mathematics software with interactive graphics, algebra and spreadsheet

https://www.geogebra.org/ || geogebra

Julia — High-level, high-performance dynamic language for technical computing.

https://julialang.org/ || julia

Kig — Application for Interactive Geometry. Part of kde-education.

https://apps.kde.org/kig/ || kig

matplotlib (PyLab) — Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.

https://www.scipy.org/ || python-matplotlib

Octave — MATLAB-like language and interface for numerical computations.

https://www.gnu.org/software/octave/ || octave

SageMath — Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.

https://www.sagemath.org/ || sagemath

Scilab — Matlab alternative used for numerical computations. Its syntax is not equivalent to that of Matlab, but it can be easily converted.

https://www.scilab.org/ || scilabAUR, scilab-binAUR, scilab-gitAUR

Statistics

gretl — A cross-platform software package for econometric analysis, written in the C programming language.

https://gretl.sourceforge.net/ || gretlAUR

JAGS (Just another Gibbs sampler) — Cross-platform program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

http://mcmc-jags.sourceforge.net/ || jagsAUR

jamovi — Statistics package, which is easy to use, and designed to be familiar to users of SPSS. Based on the Electron platform.

https://www.jamovi.org/ || jamovi-gitAUR

Python Data Analysis Library (pandas) — Providing high-performance, easy-to-use data structures and data analysis tools with Python programming language.

https://pandas.pydata.org/ || python-pandas

PSPP — Free SPSS implementation.

https://www.gnu.org/software/pspp/ || psppAUR

R — Software environment for statistical computing and graphics.

https://cran.r-project.org/ || r

RKWard — Frontend for the statistical language R.

https://rkward.kde.org/ || rkward

RStudio — A powerful and productive IDE for R written in Qt.

https://www.rstudio.com/ || rstudio-desktop-binAUR

Data analysis and plotting

AlphaPlot — Application for scientific data analysis and visualization, fork of SciDAVis / QtiPlot.

https://alphaplot.sourceforge.io/ || alphaplotAUR

DataWarrior — Open-source data visualization and analysis program with embedded chemical intelligence.

https://openmolecules.org/datawarrior/ || datawarriorAUR

Engauge Digitizer — Extracts data points from images of graphs.

https://markummitchell.github.io/engauge-digitizer/ || engaugeAUR

Fityk — Curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.

https://fityk.nieto.pl/ || fitykAUR

Gnuplot — Command-line program that can generate 2D and 3D plots of functions, data, and data fits.

http://www.gnuplot.info/ || gnuplot

Grace — WYSIWYG 2D graph plotting tool.

https://plasma-gate.weizmann.ac.il/Grace/ || graceAUR, qtgraceAUR, gracegtkAUR

KmPlot — Program to draw graphs, their integrals or derivatives. Part of kde-education.

https://apps.kde.org/kmplot/ || kmplot

LabPlot — Free software data analysis and visualization application, similar to SciDAVis.

https://labplot.kde.org/ || labplot

Plots — A graph plotting application for GNOME.

https://github.com/alexhuntley/Plots || plotsAUR

Rocs — Graph Theory IDE for everybody interested in designing and analyzing graph algorithms (e.g., lecturers, students, researchers). Part of kde-education.

https://apps.kde.org/rocs/ || rocs

ROOT — Data analysis program and library (originally for particle physics) developed by CERN.

https://root.cern.ch/ || root

See also List of applications/Documents#Spreadsheets.

Proof assistants

Physics

Physics simulation

Code_Aster — Software package for Civil and Structural Engineering finite element analysis (FEA) and numeric simulation in structural mechanics.

https://www.code-aster.org/V2/spip.php?rubrique2[dead link 2022-09-20 ⓘ] || asterAUR

OpenFOAM — Software package and toolkit for computational fluid dynamics (CFD).

https://www.openfoam.com https://openfoam.org || openfoam-orgAUR

Calculix — A three-dimensional structural finite element program.

http://www.calculix.de/ || calculix-ccxAUR

Elmer_FEM_solver — Finite element analysis (FEA/FEM) software for multiphysics problems. Includes models for fluid dynamics, structural mechanics, electromagnetics, heat transfer, and acoustics.

https://www.csc.fi/web/elmer http://www.elmerfem.org/ || elmerfemAUR

Netgen/NGSolve — A high performance multiphysics finite element software, with a flexible Python interface to implement new physical equations and solution algorithms easily.

https://ngsolve.org/ || netgen-gitAUR, ngsolve-gitAUR

ONELAB/Gmsh — An open-source, lightweight interface to finite element software, by default containing the mesh generator Gmsh, the finite element solver GetDP and the optimization library conveks.

http://onelab.info/ https://getdp.info/ https://gmsh.info/ http://onelab.info/conveks/ || gmshAUR, getdpAUR

FEniCS — An open-source computing platform for solving partial differential equations, enabling users to quickly translate scientific models into efficient finite element code with the high-level Python and C++ interfaces that scale across platforms ranging from laptops to high-performance clusters.

https://fenicsproject.org/ || dolfinAUR, python-dolfinAUR

FEBio — An open-source software tool for nonlinear finite element analysis specifically focused on solving nonlinear large deformation problems in biomechanics and biophysics, able to solve problems in mixture mechanics (i.e. biphasic or multiphasic materials), fluid mechanics, reaction-diffusion, and heat transfer, including fluid-solid interactions.

https://febio.org/ || not packaged? search in AUR

EPANET — EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.

https://www.epa.gov/ || epanet2-gitAUR

Step — Two-dimensional physics simulation engine. Part of kde-education.

https://apps.kde.org/step/ || step

SWMM — Storm Water Management Model is a dynamic rainfall-runoff-subsurface runoff simulation model used for simulation of the surface/subsurface hydrology quantity and quality.

https://www.epa.gov/ || swmm5-gitAUR

Unit conversion

ConvertAll — Unit conversion application that allows one to combine units in any way (e.g. inches per decade), even if it does not make sense.

https://convertall.bellz.org/ || convertallAUR

Gonvert — Conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.

http://www.unihedron.com/projects/gonvert/ || gonvertAUR

Units — Command-line unit converter and calculator that can handle multiplicative scale changes, nonlinear conversions such as Fahrenheit to Celsius or wire gauge and others.

https://www.gnu.org/software/units/ || units

Chemistry

Molecules

Viewers

Avogadro — Editor, viewer and simulator for 3D molecule structures (also supports downloading files from the Protein Data Bank).

https://avogadro.cc/ || avogadroAUR

BALLView — Standalone molecular modeling and visualization application, part of the BALL framework.

https://ball-project.org/ || ballAUR

Ghemical — Computational chemistry software package used to edit, view and simulate molecular structures.

http://bioinformatics.org/ghemical/ghemical/index.html || ghemicalAUR

PyMOL — Open-source molecular visualization system that can produce high quality 3D images of small molecules and biological macromolecules, such as proteins.

https://pymol.org/ || pymol

UCSF Chimera — Extensible molecular modeling system.

https://rbvi.ucsf.edu/chimera/ || ucsf-chimeraAUR

UCSF ChimeraX — Next-generation molecular visualization program, following UCSF Chimera.

https://rbvi.ucsf.edu/chimerax/ || chimeraxAUR

VMD — VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

https://www.ks.uiuc.edu/Research/vmd/ || vmdAUR

wxMacMolPlt — An open-source GUI for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package.

https://brettbode.github.io/wxmacmolplt/ || wxmacmolpltAUR

Drawing

Chemtool — GTK-based program for drawing chemical structural formulas.

http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html || chemtoolAUR

Gabedit — Graphical user interface to computational chemistry packages like GAMESS, Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, Firefly (previously PC GAMESS) and Q-Chem.

http://gabedit.sourceforge.net/ || gabeditAUR

Marvin — Java-based program for drawing chemical structural formulas.

https://chemaxon.com/marvin || marvinAUR

Modeling

AmberTools — AmberTools consists of several independently developed packages that work well by themselves, and with Amber18 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

https://ambermd.org/AmberTools.php || ambertoolsAUR

APBS — Electrostatic and solvation properties for complex molecules.

https://www.poissonboltzmann.org/ || apbsAUR

COPASI — COmplex PAthway SImulator for analysis of biochemical networks and their dynamics.

https://copasi.org/ || copasiAUR

CP2K — A quantum chemistry and solid state physics software package.

https://www.cp2k.org/ || cp2kAUR

Fpocket — Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.

https://github.com/Discngine/fpocket || fpocket-gitAUR

GROMACS (GROningen MAchine for Chemical Simulations) — Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

https://www.gromacs.org || gromacsAUR

LAMMPS — Large-scale Atomic/Molecular Massively Parallel Simulator.

https://www.lammps.org/ || lammpsAUR

MODELLER — 3D structure homology modeller.

https://salilab.org/modeller/ || modellerAUR

NAMD — NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

https://www.ks.uiuc.edu/Research/namd/ || namdAUR

NWChem — Ab initio computational chemistry software package.

https://nwchemgit.github.io/ || nwchemAUR

Open Babel — A library designed to interconvert between many file formats used in molecular modeling and computational chemistry.

https://openbabel.org/ || openbabel

ORCA — ORCA is an ab initio, DFT, and semi-empirical SCF-MO package.

https://orcaforum.kofo.mpg.de/app.php/portal || orcaqmAUR

PDB2PQR — Electrostatic and solvation properties for complex molecules.

https://www.poissonboltzmann.org/ || python-pdb2pqrAUR

PLUMED — An open source plugin for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines.

https://www.plumed.org/ || plumedAUR

PMEMD — PMEMD module of AMBER software package.

https://ambermd.org/AmberMD.php || pmemdAUR

Quantum ESPRESSO — Integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

https://www.quantum-espresso.org/ || quantum-espressoAUR

RDKit — A collection of cheminformatics and machine-learning software written in C++ and Python.

https://www.rdkit.org/ || rdkitAUR

rDock — A fast, versatile and open-source program for docking ligands to proteins and nucleic acids.

https://rdock.sourceforge.net/ || rdockAUR

smina — Smina is a fork of Autodock Vina that focuses on improving scoring and minimization.

https://sourceforge.net/projects/smina/ || smina-binAUR

Simulation analysis

mdanalysis — An object-oriented python toolkit to analyze molecular dynamics trajectories in many popular formats.

https://www.mdanalysis.org || python-mdanalysisAUR

MDTraj — A modern, open library for the analysis of molecular dynamics trajectories.

https://github.com/mdtraj/mdtraj || python-mdtrajAUR

xdrfile — Allows to read GROMACS trr and xtc files and also to convert from one format to another.

https://manual.gromacs.org/current/reference-manual/file-formats.html#xdr || xdrfileAUR

Periodic table

eperiodique — A simple Periodic Table Of Elements viewer using the EFL.

http://eperiodique.sourceforge.net/ || eperiodiqueAUR

gElemental — Periodic table of the elements with additional information.

https://freshmeat.sourceforge.net/projects/gelemental || gelementalAUR

Kalzium — Periodic table of the elements with molecule editor and equation solver. Part of kde-education.

https://apps.kde.org/kalzium/ || kalzium

Earth science

Geography

BT747 — The swiss army knife for MTK GPS dataloggers.

https://sourceforge.net/projects/bt747/ || bt747

FoxtrotGPS — Lightweight and fast mapping application.

https://www.foxtrotgps.org/ || foxtrotgpsAUR

Gebabbel — Alternative GUI for GPSBabel.

http://gebabbel.sourceforge.net/ || gebabbelAUR

GeoDa — A tool for spatial data analysis.

https://geodacenter.github.io/ || geoda-binAUR

GNOME Maps — A simple map client for GNOME. Part of gnome-extra.

https://wiki.gnome.org/Apps/Maps || gnome-maps

Gpredict — Real-time satellite tracking and orbit prediction application.

http://gpredict.oz9aec.net/ || gpredictAUR

GPSBabel — Reads, writes, and manipulates GPS waypoints, tracks, routes in a variety of formats.

https://www.gpsbabel.org/ || gpsbabel

gpsd — Service daemon that monitors one or more GPSes or AIS receivers attached to a host computer through serial or USB ports, making all data on the location/course/velocity of the sensors available to be queried on TCP port 2947 of the host computer.

http://catb.org/gpsd/ || gpsd

GpsPrune — View, edit and convert coordinate data from GPS systems.

https://activityworkshop.net/software/gpsprune/ || gpsprune

GPXSee — GPS log file viewer and analyzer.

https://www.gpxsee.org/ || gpxsee

GPX Viewer — Simple tool to visualize tracks and waypoints stored in a gpx file.

https://blog.sarine.nl/tag/gpxviewer/ || gpx-viewer

GRASS GIS — Geospatial data management and analysis, image processing, graphics/maps production, spatial modeling and visualization.

https://grass.osgeo.org/ || grassAUR

gvSIG — vSIG is a geographic information system (GIS), that is, a desktop application designed for capturing, storing, handling, analyzing and deploying any kind of referenced geographic information in order to solve complex management and planning problems.

http://www.gvsig.com/en || gvsig-desktop-binAUR

JOSM — Main editor for OpenStreetMap written in Java.

https://josm.openstreetmap.de/ || josm

Mapton — Extensible desktop map and globe application written in Java.

https://mapton.org/ || maptonAUR

Marble — Virtual Globe and World Atlas that can be used to learn more about the Earth. Part of kde-education.

https://marble.kde.org/ || KDE: marble, Qt: marble-qt

Merkaartor — OpenStreetMap editor.

http://merkaartor.be/ || merkaartor

Navit — Modular turn-by-turn car navigation system.

https://www.navit-project.org/ || navit

OffRoad — Offline vector map display ported from OsmAnd.

https://sourceforge.net/projects/offroadosm/ || offroad

OpenOrienteering Mapper — Orienteering mapmaking program.

https://www.openorienteering.org/apps/mapper/ || openorienteering-mapperAUR

QMapShack — Plan your next outdoor trip.

https://github.com/Maproom/qmapshack/ || qmapshack

QGIS — Geographic Information System (GIS) that supports vector, raster & database formats.

https://qgis.org/ || qgis

Subsurface — Diving logbook to keep track of your dives by logging dive locations (with GPS coordinates), weights and exposure protection used, divemasters and dive buddies, etc.

https://subsurface-divelog.org/ || subsurfaceAUR

Viking — GTK 2 application to manage GPS data.

https://sourceforge.net/projects/viking/ || viking

Meteorology

Gis Weather — Customizable weather forecast desktop widget.

https://sourceforge.net/projects/gis-weather/ || gis-weatherAUR

GNOME Weather — Small application for GNOME that allows you to monitor the current weather conditions for your city, or anywhere in the world, and to access updated forecasts provided by various internet services.

https://wiki.gnome.org/Apps/Weather || gnome-weather

meteo-qt — System tray application for weather status information.

https://github.com/dglent/meteo-qt || meteo-qtAUR

wttr — A simple console application to check the weather, using data from https://wttr.in

https://github.com/AmirrezaFiroozi/wttr || wttrAUR

Xfce Weather Panel Plugin — Weather forecast plugin for the Xfce4 panel.

https://goodies.xfce.org/projects/panel-plugins/xfce4-weather-plugin || xfce4-weather-plugin

wego — A terminal weather application.

https://tylerwolf35.github.io/wego || wegoAUR

Astronomy

Astropy — The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages.

https://www.astropy.org/ || python-astropy

Celestia — 3D astronomy simulation program that allows users to travel through an extensive universe, modeled after reality, at any speed, in any direction and at any time in history.

https://celestia.space/ || celestiaAUR

GIMP Astronomy Plugins — Set of GIMP plugins for astronomical image processing.

http://hennigbuam.de/georg/gimp.html || gimp-plugin-astronomyAUR

GoQat — Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.

https://canburytech.net/GoQat/ || goqatAUR

KStars — Planetarium application that provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time. It is included in KDE Edu.

https://apps.kde.org/kstars/ || kstars

Skychart / Cartes du Ciel — Planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.

https://www.ap-i.net/skychart/ || skychart-binAUR

SPICE — A comprehensive toolkit and api to design, simulate and analyse space missions

https://naif.jpl.nasa.gov/naif/index.html || cspiceAUR

StarPlot — 3-dimensional star chart viewer.

http://starplot.org/ || starplotAUR

Stellarium — Beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.

https://stellarium.org/ || stellariumAUR

XEphem — Motif-based ephemeris and planetarium program.

https://xephem.github.io/XEphem/Site/xephem.html || xephemAUR

Biology

Computational biology and bioinformatics

BALL (Biochemical Algorithms Library) — Application framework in C++ that provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

https://ball-project.org/ || ballAUR

BioJava — Set of Java tools for computational biology, as well as bioinformatics.

https://biojava.org/ || biojavaAUR

Biopython — Python package with tools for computational biology, as well as bioinformatics.

https://biopython.org/wiki/Biopython || python-biopython

EMBOSS (European Molecular Biology Open Software Suite) — Open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community.

https://emboss.sourceforge.net/ || embossAUR

MUMmer — Bioinformatics software system for sequence alignment based on suffix trees.

https://mummer.sourceforge.net/ || mummerAUR

Snapgene — Closed source molecular cloning application that offers a fast and easy way to plan, visualize, and document molecular biology procedures. Supports a wide range of cloning and PCR manipulations. The free version allows most common visualizations of a molecular biology workflow.

https://www.snapgene.com/ || snapgene-viewerAUR

UGENE — Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.

https://ugene.net/ || ugene-binAUR, ugene-gitAUR

Genealogy

Gramps — Genealogy program, which helps you track your family tree.

https://gramps-project.org/ || gramps

LifeLines — Text based genealogy software for family trees and reports.

https://github.com/lifelines/ || lifelinesAUR

Image manipulation

ImageJ — Java-based image processing and analysing program that provides extensibility via plugins and macros. It is widely used in microscopy (e.g. for cell counting).

https://imagej.nih.gov/ij/ || imagejAUR

Fiji — ImageJ distribution (and soon ImageJ2) with a lot of plugins organized into a coherent menu structure.

https://fiji.sc || fiji-binAUR

DICOM viewers and volume rendering

aeskulap — Simple DICOM data viewer

https://www.nongnu.org/aeskulap/ || aeskulapAUR

weasis — Multipurpose DICOM viewer with a highly modular architecture

https://nroduit.github.io/en/ || weasis-binAUR

aliza — Open 2D, 3D and 4D images in DICOM, MetaIO, Nifti, Nrrd and other formats, meshes in DICOM, VTK, STL and OBJ formats

https://www.aliza-dicom-viewer.com/ || alizaAUR

3DSlicer — Comprehensive MRI, CT, LSCM microscopy volume processing, segmentation and 3D-reconstruction

https://www.slicer.org/ || 3dslicerAUR

ParaView — Interactive data visualization tool built using VTK that can scale across distributed computer hardware.

https://www.paraview.org/ || paraview

Engineering

Computer-aided design

BRL-CAD — Constructive solid geometry modeling CAD system that includes an interactive geometry editor, ray tracing support for graphics rendering and geometric analysis, computer network distributed framebuffer support, scripting, image-processing and signal-processing tools.

https://brlcad.org/ || brlcadAUR

FreeCAD — Parametric 3D CAD modeler based on OpenCascade, Coin3D, Qt, and Python with features such as macro recording, workbenches and the ability to run as a server.

https://freecadweb.org/ || freecad

LeoCAD — CAD program for creating virtual LEGO models. It has an easy to use interface and currently includes over 10,000 different pieces created by the LDraw community.

https://www.leocad.org/ || leocad

LibreCAD — A 2D CAD application based on Qt5. Forked from QCAD Community Edition.

https://www.librecad.org/ || librecad

OpenSCAD — A 3D CAD modeler that uses a textual, programmatic approach to creating and manipulating objects.

https://www.openscad.org || openscad

QCAD — A 2D CAD application based on Qt. Supports the DFX and HPGL standard file formats, and optionally the DWG format through a proprietary plugin.

https://www.qcad.org/ || qcad

SolveSpace — Powerful 3D CAD constraint-based parametric modeler with simple mechanical simulation capabilities.

https://solvespace.com/ || solvespaceAUR

3D printing

Telecommunication

GNU Radio — Software development toolkit that provides signal processing blocks to implement software radios.

https://www.gnuradio.org/ || gnuradio

Gqrx — Software defined radio receiver implemented using GNU Radio and the Qt GUI toolkit.

https://gqrx.dk/ || gqrx

Pothos — The Pothos project is a complete data-flow framework for creating topologies of interconnected processing blocks.

https://github.com/pothosware/PothosCore/wiki || pothosAUR, pothos-gitAUR

SDR# — The most popular SDR program.

https://airspy.com/ || sdrsharpAUR

SigDigger — Qt-based digital signal analyzer, using Suscan core and Sigutils DSP library.

https://github.com/BatchDrake/SigDigger || sigdigger-gitAUR

Amateur radio

See the main article: Amateur radio#Software list.

Simulation modeling

Flight Gear — Open-source, multi-platform atmospheric and orbital flight simulator with a flight dynamics engine (JSBSim) that is part of a 2015 NASA benchmark to judge new simulation code to space industry standards.

https://www.flightgear.org/ || flightgearAUR

gephi — Gephi is an open-source network analysis and visualization software package written in Java.

https://gephi.org/ || gephi

golly — Golly is an open source, cross-platform application for exploring Conway's Game of Life and many other types of cellular automata.

https://golly.sourceforge.net/ || gollyAUR

Netlogo — NetLogo is a multi-agent programmable modeling environment.

http://ccl.northwestern.edu/netlogo/ || netlogoAUR

AnyLogic — AnyLogic is a cross-platform proprietary multimethod simulation modeling tool, which is also available for personal use.

https://www.anylogic.com/ || anylogic-pleAUR, anylogic-universityAUR, anylogic-professionalAUR

Computer science

Architecture

edumips64 — Cross-platform educational MIPS64 CPU simulator.

https://edumips.org/ || edumips64AUR

Qiskit Aer — A high performance simulator for quantum circuits that includes noise models.

https://github.com/Qiskit/qiskit-aer || python-qiskit-aer-gpuAUR

QtMips — MIPS CPU simulator for education purposes with pipeline and cache visualization.

https://github.com/cvut/QtMips || qtmipsAUR

QtRvSim — RISC-V CPU simulator for education purposes.

https://github.com/cvut/qtrvsim || qtrvsimAUR

Artificial intelligence

Fast Artificial Neural Network — Library for developing feedforward Artificial Neural Networks.

http://leenissen.dk/fann/wp/ || fannAUR

Mycroft — Intelligent personal assistant and knowledge navigator with speech recognition.

https://mycroft.ai/ || mycroft-coreAUR

Orange — Data visualization, machine learning and data mining toolkit, accessible via visual programming and Python.

https://orange.biolab.si/ || python-orangeAUR

Torch — Machine learning library, scientific computing framework, and script language based on LuaJIT.

http://torch.ch/ || torch7-gitAUR

X Neural Switcher — Automatic (intelligent) keyboard layout adaption.

https://xneur.ru/ || xneur-devel-gitAUR, gxneurAUR

Tensorflow — An end-to-end open source machine learning platform.

https://www.tensorflow.org/ || python-tensorflow, with non x86-64 CPU optimization python-tensorflow-opt, with CUDA python-tensorflow-cuda, with CUDA and with non x86-64 CPU optimizations python-tensorflow-opt-cuda

PyTorch — An open source machine learning framework that accelerates the path from research prototyping to production deployment.

https://pytorch.org/ || python-pytorch, with CUDA python-pytorch-cuda

Theano — Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.

http://deeplearning.net/software/theano/ || python-theanoAUR

Distributed systems