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Revision as of 21:58, 24 November 2010 by Alexlan (talk | contribs) (→‎Biology / Bioinformatics Software: add packages now in collection from wishlist)

List of scientific/engineering packages


  • Please check out the separate page.

Biology / Bioinformatics Software

Package Name Description
bwa Burrows-Wheeler Alignment Tool for efficient short read alignment (original Review Request)
elph Tool to find motifs in a set of DNA or protein sequences
EMBOSS Hundreds of useful, well documented applications for molecular sequence and other analyses.
glimmer System for finding genes in microbial DNA
hmmer Profile HMM software for protein sequence analysis
lagan Local, global, and multiple alignment of DNA sequences
perl-bioperl A collection of tools for bioinformatics in Perl
perl-biopython A collection of tools for bioinformatics in Python
SAMtools SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
seaview Graphical multiple sequence alignment editor
SIBsim4 Align expressed RNA sequences on a DNA template
pipviewer Visualizer for multiple alignments of genomic sequences
PyPop Software for analyzing population genomics data
vhybridize Virtual Hybridization command line tools
ugene Genome analysis suite


Package Name Description
Avogadro An advanced molecular editor for chemical purposes
GChemistry Gnome Chemistry Utils incl. periodic table of the elements, molecular structure viewer and chemical calculator
gromacs Gromacs - Fast, Free and Flexible MD
inchi The IUPAC International Chemical Identifier library
jmol An open-source Java viewer for chemical structures in 3D
openbabel Chemistry software file format converter
pymol PyMOL Molecular Viewer
PyQuante Python Quantum Chemistry
xdrawchem 2D chemical structures drawing tool
BKChem chemical drawing program
Kalzium Period table, chemsitry calculator, etc.

Electrical engineering

Package Name Description
The Geda Suite The complete suite for Electrical schematic and simulation
Documentation for gEDA
Circuit examples for gEDA
Attribute editor for gEDA
Netlister for the gEDA project
Electronics schematics editor
Symbol checker for electronics schematics editor
A bunch of symbols of electronic devices used by gschem.
Utilities for gEDA
gresistor To allow for identification, resistors are usually marked with colored bands. Often refereed to as color codes, these markings are indicative of their resistance, tolerance and temperature coefficient.
gnucap GNU Circuit Analysis Package
ktechlab Development and simulation of microcontrollers and electronic circuits
Ngspice A mixed level/signal circuit simulator
pcb PCB is an interactive printed circuit board editor for the X window system.
toped IC Layout Editor
xcircuit Xcircuit is a general-purpose drawing program and also a specific-purpose CAD program for circuit schematic drawing and schematic capture.
qucs Qucs is a circuit simulator with graphical user interface. The software aims to support all kinds of circuit simulation types, e.g. DC, AC, S-parameter and harmonic balance analysis.
freehdl A project to develop a free, open source, GPL'ed VHDL simulator for Linux.


Package Name Description
Armadillo fast C++ matrix library with interfaces to LAPACK and ATLAS
blitz Blitz++ is a C++ class library for matrix scientific computing
calc Calc is an arbitrary precision C-like arithmetic system that is a calculator, an algorithm-prototyper, and a mathematical research tool.
kpolynome KPolynome is a program to calculate mathematical polynomes based on given data coordinates.
mona Mona is a decision procedure for the WS1S and WS2S logics
Octave Octave is a Matlab-Clone
R R is a software environment for statistical computing and graphics
scigraphica Scientific application for data analysis and technical graphics

Mechanical engineering

Package Name Description
FreeFEM Free<Fem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily.
Qcad QCad is an application for computer aided drafting in two dimensions (2d)


Package Name Description
gromacs Gromacs - Fast, Free and Flexible MD
jmol An open-source Java viewer for chemical structures in 3D
openbabel Chemistry software file format converter
pymol PyMOL Molecular Viewer