applications/engineering
- BEDTools - A flexible suite of utilities for comparing genomic features
- ColPack - Algorithms for specialized vertex coloring problems
- GMT - Generic Mapping Tools
- GMT-coastlines - Coastline data for GMT
- Macaulay2 - System for algebraic geometry and commutative algebra
- PyQuante - Python Quantum Chemistry
- R - A language for data analysis and graphics
- R-DBI - Database interface module for R
- R-RM2 - Revenue Management and Pricing for R
- R-RScaLAPACK - An interface to perform parallel computation on linear algebra problems using ScaLAPACK
- R-car - Companion to Applied Regression package for R
- R-hdf5 - Interface to the NCSA HDF5 library
- R-lmtest - Testing Linear Regression Models for R
- R-msm - Multi-state Markov and hidden Markov models in continuous time
- R-multcomp - Simultaneous inference for general linear hypotheses R Package
- R-mvtnorm - Multivariate normal and T distribution R Package
- R-qtl - Tools for analyzing QTL experiments
- R-systemfit - Simultaneous Equation Estimation R Package
- R-zoo - Z's ordered observations for irregular time series
- alliance - VLSI EDA System
- apbs - Adaptive Poisson Boltzmann Solver
- archimedes - 2D Quantum Monte Carlo simulator for semiconductor devices
- avarice - Program for interfacing the Atmel JTAG ICE to GDB
- bfast - Blat-like Fast Accurate Search Tool
- bowtie - An ultrafast, memory-efficient short read aligner
- bwa - Burrows-Wheeler Alignment tool
- cddlib - A library for generating all vertices in convex polyhedrons
- chntpw - Change passwords in Windows SAM files
- clac - Command Line Advanced Calculator
- dgc - Digital Gate Compiler
- dia-CMOS - Dia CMOS Shapes
- dia-Digital - Dia Digital IC logic shapes
- dia-electric2 - Dia Digital IC logic shapes
- dia-electronic - Dia Digital IC logic shapes
- dinotrace - Waveform viewer for electronics
- drgeo - Interactive educational geometry software
- drgeo-doc - Html documentation for drgeo
- ds9 - Astronomical Data Visualization Application
- dx - Open source version of IBM's Visualization Data Explorer
- electric - Sophisticated Java based VLSI CAD System
- emacs-verilog-mode - Verilog mode for Emacs
- eqntott - Generates truth tables from Boolean equations
- ergo - A program for large-scale self-consistent field calculations
- espresso-ab - A boolean minimization tool
- freehdl - GPLed free VHDL
- funtools - FITS library and utilities
- gabedit - GUI for computational chemistry
- gdl - GNU Data Language
- geda-gaf - Design Automation toolkit for electronic design
- geomview - Interactive 3D viewing program
- geos - GEOS is a C++ port of the Java Topology Suite
- gerbv - Gerber file viewer from the gEDA toolkit
- gnucap - The Gnu Circuit Analysis Package
- gperiodic - Program for browsing the periodic table
- gplcver - An interpreted Verilog HDL simulator
- grace - Numerical Data Processing and Visualization Tool
- grads - Tool for easy acces, manipulation, and visualization of data
- gromacs - Fast, Free and Flexible Molecular Dynamics
- gtkwave - Waveform Viewer
- iec16022 - Generate ISO/IEC 16022 2D barcodes
- irsim - Switch-level simulator used even for VLSI
- iverilog - Icarus Verilog is a verilog compiler and simulator
- jmol - An open-source Java viewer for chemical structures in 3D
- kst - A data viewing program for KDE
- lcm - Utilities for lightweight communications and marshaling
- libxc - Library of exchange and correlation functionals to be used in DFT codes
- linsmith - A Smith charting program
- lis - A library for solving linear equations and eigenvalue problems
- magic - A very capable VLSI layout tool
- maloc - Minimal Abstraction Layer for Object-oriented C
- maxima - Symbolic Computation Program
- messiggy - Messiggy is a database of celestial objects
- mmseq - Haplotype and isoform specific expression estimation for RNA-seq
- ncl - NCAR Command Language and NCAR Graphics
- nco - Suite of programs for manipulating NetCDF/HDF4 files
- nesc - Compiler used by TinyOS
- netcdf - Libraries for the Unidata network Common Data Form (NetCDF v3)
- netcdf-decoders - Converts WMO GRIB products into NetCDF files
- netgen - LVS netlist comparison tool for VLSI
- ngspice - A mixed level/signal circuit simulator
- normaliz - A tool for mathematical computations
- octave - A high-level language for numerical computations
- octave-forge - Contributed functions for octave
- ogdi - Open Geographic Datastore Interface
- openscada - Open SCADA system project
- pcb - An interactive printed circuit board editor
- perl-Verilog - Verilog parsing routines
- perl-Verilog-Perl - Verilog parsing routines
- plplot - Library of functions for making scientific plots
- proj - Cartographic projection software (PROJ.4)
- pygrace - Python bindings for grace
- pymol - PyMOL Molecular Graphics System
- qd - Double-Double and Quad-Double Arithmetic
- qucs - Circuit simulator
- root - Numerical data analysis framework
- roundup - Simple and flexible issue-tracking system
- samtools - Tools for nucleotide sequence alignments in the SAM format
- sextractor - Extract catalogs of sources from astronomical images
- tachyon - Parallel / Multiprocessor Ray Tracing System
- teal - Verification Utility and Connection Library
- tkgate - An event driven digital circuit simulator
- toped - VLSI IC Layout Editor
- towhee - A Monte Carlo molecular simulation code
- vcftools - VCF file manipulation tools
- vhd2vl - VHDL to Verilog translator
- vrq - Verilog tool framework with plugins for manipulating source code
- wannier90 - Maximally-localised Wannier functions
- wcstools - Software utilities to display and manipulate the WCS of a FITS image
- wgrib - Manipulate, inventory and decode GRIB files
- wgrib2 - Manipulate, inventory and decode GRIB2 files
- wxMaxima - Graphical user interface for Maxima
- xcircuit - Electronic circuit schematic drawing program
- xdrfile - A small C-library for reading and writing GROMACS trr and xtc files
- xpa - The XPA messaging system
- xvarstar - XVarStar is an astronomical program used for searching GCVS