WEKA 3.6.0

A data mining workbench in Java.

developer: eibe
version: 3.6.0
license: GPL
updated: 2009-04-26
downloads: 31852
Jmol 12.2.10

Jmol is a (bio)molecular viewer applet and application.

developer: Egon Willighagen and Michael Howard
version: 12.2.10
license: LGPL
updated: 2011-12-22
downloads: 7118
Bioperl 1.6.0_4

A Perl extensions for bioinformatics.

developer: Bioperl developers
version: 1.6.0_4
license: Artistic License
updated: 2009-09-28
downloads: 6814
THCcalc 1.2.1

THCcalc calculates the THC content in a person's blood based on their usage pattern over a...

developer: Eric Fenderson
version: 1.2.1
license: Public Domain
updated: 2006-01-03
downloads: 6510
Geant4 4.9.5 Beta

A toolkit for the simulation of the passage of particles through matter.

developer: Geant4 Development Team
version: 4.9.5 Beta
license: GPL
updated: 2011-08-31
downloads: 3573
Ghemical 2.95

Ghemical is a molecular modelling package with GUI and 3D-visualization tools.

developer: TH
version: 2.95
license: GPL
updated: 2007-09-25
downloads: 3114
VULCAN 6.0.1

VULCAN project provides computational fluid dynamics analysis.

developer: Hypersonic Airbreathing Propulsion Branch Of NASA
version: 6.0.1
license: Other
updated: 2007-09-21
downloads: 2442
E-Cell System 3.2.2

A modelling and simulation software environment.

developer: Kouichi Takahashi
version: 3.2.2
license: GPL
updated: 2011-10-26
downloads: 1957
COPASI 4.6 Build 32

A tool for simulation and modeling of biochemical networks.

developer: Pedro Mendes, Virginia Tech Intellectual Properties, Inc. and EM
version: 4.6 Build 32
license: Free for non-commerc...
updated: 2010-07-22
downloads: 1716
CLC Main Workbench 5.0

A software environment enabling users to make a large number of advanced protein sequence analyse

developer: CLC bio A/S
version: 5.0
license: Shareware
updated: 2009-01-30
downloads: 1663
Geneious 5.3 / 5.5 Beta

Geneious greatly speeds up and simplifies research in molecular biology and biochemistry.

developer: Biomatters Ltd.
version: 5.3 / 5.5 Beta
license: Free for non-commerc...
updated: 2011-08-31
downloads: 1647
BALLView 1.4.0

BALLView is an extensible viewer for bio-molecular structures.

developer: Andreas Moll
version: 1.4.0
license: GPL
updated: 2010-12-10
downloads: 1588
CLC Sequence Viewer 5.0

CLC Sequence Viewer is a bioinformatics program for DNA, RNA, and protein sequence analysis

developer: CLC bio A/S
version: 5.0
license: Freeware
updated: 2008-07-03
downloads: 1440
ESTScan 3.0.3

Detect coding regions in DNA sequences, even if they are of low quality

developer: Christian Iseli
version: 3.0.3
license: Other
updated: 2009-06-17
downloads: 1421
Raster3D 2.7s

Raster3D is a powerful set of tools for generating high quality raster images of proteins or...

developer: Biomolecular Structure Center at the University of Washington
version: 2.7s
license: Other
updated: 2008-04-22
downloads: 1388
Bioclipse 2.0

A rich-client platform chemistry and biology workbench.

developer: Bioclipse Team
version: 2.0
license: Eclipse Public License
updated: 2009-07-09
downloads: 1384
massXpert mass spectrometry package 3.2.0

A mass spectrometry environment for linear (bio-) polymers.

developer: Filippo Rusconi
version: 3.2.0
license: GPL v3
updated: 2011-10-24
downloads: 1370
ploticus 2.41

A graphics, charting, and plot presentation package.

developer: Stephen Grubb
version: 2.41
license: GPL
updated: 2009-03-12
downloads: 1227
Bioinformatics Benchmark System 3

Bioinformatics Benchmark System is a bioinformatics benchmark system for platform performance...

developer: Joe Landman
version: 3
license: GPL
updated: 2005-08-13
downloads: 1051
BioJava 1.30

BioJava is an open source Java components for biological computation.

developer: Thomas Down
version: 1.30
license: LGPL
updated: 2005-04-01
downloads: 1046
BndLst 1.6.001127

Bndlst is a PDB file format reader.

developer: Kinemage
version: 1.6.001127
license: GPL
updated: 2008-05-08
downloads: 1041
Java Machine Learning Library 0.1.6

A set of reference implementations of machine learning algorithms.

developer: Thomas Abeel
version: 0.1.6
license: GPL
updated: 2010-10-18
downloads: 998
Array Designer 4.11

Array Designer helps design thousands of efficient, highly specific oligos to make microarrays...

developer: PREMIER Biosoft International
version: 4.11
license: Shareware
updated: 2006-01-13
downloads: 979
Mauve 2.3.1

Constructs global multiple alignments of rearranged genome sequences

developer: Aaron Darling
version: 2.3.1
license: GPL
updated: 2009-11-12
downloads: 926
CodonW 1.4.4

CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis)...

developer: John Peden
version: 1.4.4
license: GPL
updated: 2008-04-24
downloads: 866
Isotopic Pattern Calculator 1.4

Isotopic Pattern Calculator is a calculates isotopic distributions.

developer: Dirk Nolting
version: 1.4
license: GPL
updated: 2005-08-15
downloads: 859
Murka 1.1.10

Software for working with median networks and Steiner trees from alignments of biological sequences.

developer: Valery Zaporozhchenko
version: 1.1.10
license: LGPL
updated: 2009-05-09
downloads: 838
GApop 0.1

GApop is a genetic algorithm external for PD and MAX/MSP, written in C .

developer: Georg Holzmann
version: 0.1
license: GPL
updated: 2008-04-12
downloads: 789
Slice Tools 2.0.0

Slice Tools is a genomic assembly manipulation toolkit.

developer: Michael Schatz
version: 2.0.0
license: GPL
updated: 2007-12-21
downloads: 770
HTSeq 0.5.3p3

Processing high-throughput sequencing data with Python

developer: Simon Anders
version: 0.5.3p3
license: GPL
updated: 2011-09-16
downloads: 770
NSCL SpecTcl 3.0-013 / 3.1-005 / 3.2-pre3

SpecTcl is a framework for data analysis of nuclear physics event data.

developer: Ron Fox
version: 3.0-013 / 3.1-005 / 3.2-pre3
license: GPL
updated: 2008-01-29
downloads: 750
mpiBLAST 1.4.0-pio / 1.5.0 Beta 1

mpiBLAST is an MPI based parallel implementation of NCBI BLAST.

developer: mpiBLAST team
version: 1.4.0-pio / 1.5.0 Beta 1
license: GPL
updated: 2007-12-20
downloads: 727
PathVisio 2.0.11

Easily display and edit biological pathways

developer: PathVisio
version: 2.0.11
license: The Apache License 2.0
updated: 2011-02-25
downloads: 719
JOELib/JOELib2 2007-03-03

JOELib/JOELib2 is a Java-based chemoinformatics library.

developer: Joerg K. Wegner
version: 2007-03-03
license: GPL
updated: 2007-03-03
downloads: 715
wEMBOSS 2.1.1

A web interface to the popular EMBOSS software

developer: The wEMBOSS team
version: 2.1.1
license: GPL
updated: 2009-06-23
downloads: 693
BEAST 1.4.7

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.

developer: Alexei Drummond and Andrew Rambaut
version: 1.4.7
license: GPL
updated: 2008-05-06
downloads: 686
ByoDyn 5.3

An integrative tool for Systems Biology.

developer: Adrián L. García de Lomana and Jordi Villà-Freixa
version: 5.3
license: GPL
updated: 2009-03-20
downloads: 674
Fura 1.5.6

Fura is a self-contained grid middleware that allows the grid enablement and distribution of...

developer: Grid Systems, S.A.
version: 1.5.6
license: GPL
updated: 2009-03-23
downloads: 673
PDBCat 1.3

PDBCat it manipulates PDB molecule files with text-based tools such as Perl, awk, etc.

developer: Andrew Dalke
version: 1.3
license: Freely Distributable
updated: 2005-04-01
downloads: 664
Adun 0.8.2

Adun is an extensible biomolecular simulation program that includes data management and analysis...

developer: The Adun developers
version: 0.8.2
license: GPL
updated: 2008-01-22
downloads: 661
GDIS 0.89

GDIS is a GTK based program for the display and manipulation of isolated molecules and periodic...

developer: Sean Fleming
version: 0.89
license: GPL
updated: 2008-02-12
downloads: 646

RIPCAL is a bio-informatics software for the analysis of repeat-induced point mutation (RIP)...

developer: ACNFP Bioinformatics
version: 2.0
license: Academic Free License
updated: 2009-06-17
downloads: 644
MacMolPlt 7.1

MacMolPlt is a modern graphics program for plotting 3-D molecular structures and normal modes...

developer: Brett Bode
version: 7.1
license: GPL
updated: 2008-04-08
downloads: 633
Annotathon 0.2

Bioinformatics training through metagenomic sequence annotation.

developer: hingamp
version: 0.2
license: GPL v3
updated: 2008-09-26
downloads: 618
semanticSBML 1.0.9

A tool that can create, check, annotate, merge SBML (System Biology Markup Language) models

developer: Computational Systems Biology
version: 1.0.9
license: GPL
updated: 2009-07-17
downloads: 596
QTL Reaper 1.1.1

QTL Reaper is software for rapidly scanning microarray expression data for QTLs.

developer: Ken Manly and J. Wang
version: 1.1.1
license: GPL
updated: 2008-03-20
downloads: 587
Systems Biology Workbench 2.5.5

Systems Biology Workbench (SBW) is a simple framework for application intercommunications.

developer: Keck Graduate Institute
version: 2.5.5
license: BSD License
updated: 2008-01-14
downloads: 575
nwalign 0.3.0

Needleman-Wunsch global sequence alignment in Python

developer: Brent Pedersen
version: 0.3.0
license: BSD License
updated: 2009-12-28
downloads: 574
Quick-Join 1.0.10

QuickJoin implements a heuristic for speeding up neighbour joining, making neighbour joining...

developer: Thomas Mailund
version: 1.0.10
license: GPL
updated: 2008-01-23
downloads: 574
The Digital Seed Vault 0.5.0

A seed stock database mainly developed for researchers in the plant sciences

developer: Myckel Habets
version: 0.5.0
license: GPL v3
updated: 2010-03-11
downloads: 563
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