Revision as of 21:58, 24 November 2010

List of scientific/engineering packages

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.

Package Name	Description
The Geda Suite	The complete suite for Electrical schematic and simulation
geda-docs geda-examples geda-gattrib geda-gnetlist geda-gschem geda-gsymcheck geda-symbols geda-utils	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

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

@@ Line 10: / Line 10: @@
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 !'''Package Name'''||'''Description'''
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+|  [http://bio-bwa.sourceforge.net/ bwa] || Burrows-Wheeler Alignment Tool for efficient short read alignment ([https://bugzilla.redhat.com/show_bug.cgi?id=597315 original Review Request])
 |-
 | [http://www.cbcb.umd.edu/software/ELPH/ elph] || Tool to find motifs in a set of DNA or protein sequences
+|-
+| [http://emboss.sourceforge.net/ EMBOSS] || Hundreds of useful, well documented applications for molecular sequence and other analyses.
 |-
 | [http://www.cbcb.umd.edu/software/glimmer glimmer] || System for finding genes in microbial DNA
@@ Line 22: / Line 26: @@
 |-
 | [http://www.biopython.org/ perl-biopython] || A collection of tools for bioinformatics in Python
+|-
+| [http://samtools.sourceforge.net/ SAMtools] || SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.
 |-
 | [http://pbil.univ-lyon1.fr/software/seaview.html seaview] || Graphical multiple sequence alignment editor
@@ Line 28: / Line 34: @@
 |-
 | [http://ygingras.net/bioinfo pipviewer] || Visualizer for multiple alignments of genomic sequences
+|-
+| [http://www.pypop.org/ PyPop] || Software for analyzing population genomics data
 |-
 | [http://ygingras.net/bioinfo vhybridize] || Virtual Hybridization command line tools