Accelrys
Software and service solutions to pharmaceutical, biotechnology, and industrial chemical research organizations.
Array Designer
Microarray design, oligo and cDNA
Array Genetics
Online bioinformatics products
BAMBE
Bayesian Analysis in Molecular Biology and Evolution
Bioconductor
Open source and open development software project
for the analysis and comprehension of genomic data
BioPython
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
BioWarehouse
Integrate multiple public bioinformatics databases into a single relational database system.
Boost
Boost provides free peer-reviewed portable C++ source libraries
Chromas
Opens chromatogram files from Applied Biosystems, Amersham MegaBace DNA sequencers, ALF, Li-Cor, Visible Genetics OpenGene, Beckman CEQ 2000XL, CEQ 8000, and other sequencers. Save in SCF or Applied Biosystems format.
Cytoscape
Open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data
Decodon
Software tools for functional genomics
eBioinformatics
Bioinformatics tools for MacOSX
Eplore any 3D macromolecular structure model
Protein Explorer in Chime, FirstGlance in Jmol
ERGO integrated genomics
Comprehensive genome analysis including genomic, biochemical data, literature, and high-throughput analysis
ExploRase
R tool for the exploratory multivariate analysis of Systems Biology data
FirstGlance in Jmol
Macromolecular visualization with exceptional ease of use.
Folding@Home
Screensaver that donates CPU time to solving protein folding problems. (Similar to SETI@home)
GeneSifter
Microarray analysis: makes it easier to understand the biological significance of your microarray data using the latest annotation and statistics
Genestudio
GenMAPP - Gene MicroArray Pathway Profiler
Visualize gene expression data on maps representing biological pathways and groupings of genes
GenoWiz
Microarray analysis: store, process and visualize gene expression data
GGobi
Data visualization system for viewing high-dimensional data
GON - Genomic Object Net Pathway Database
Software platform for biological pathway modeling and simulation, based on hybrid functional Petri net (HFPN) and XML technology
Google directory for bioinformatics software
HTS Tools
High Throughput Screening (HTS) analysis
INCLUsive
INCLUSive is suite of web-based tools and is aimed at the automatic multistep analysis of microarray data.
ISYS - Integrated SYStem
Dynamic, flexible open source platform for the integration of bioinformatics software tools and databases
Java GBrowse
Java GBrowse is a Java Applet-based implementation of the original CGI-based GMOD GBrowse web application developed by GMOD
JCell - Gene regulatory networks
Java based framework to reconstruct genetic interactions from microarray data
JigCell
open source modeling environment for computational biology
KegTools
KegHier, KegArray and KegDraw
KoriBlast
KoriBlast is a reliable graphical environment dedicated to Blast data mining.
MEGA Software
Molecular Evolutionary Genetics Analysis
MetNet project
The MetNet project for analyzing experimental data in the context of metabolic and regulatory networks
miRanda
microRNA Target Detection
MolTalk
A computational environment for Structural Bioinformatics
MUPRED
Protein Secondary Structure Prediction Software
National Center for Biotechnology Information
A national resource for molecular biology information. Creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information.
Page lab software review
ParseBioNet
Metabolic Data Modelling
Pathway Tools
Genome-scale manipulation of metabolic pathways and transcriptional regulatory networks.
pDRAW32
DNA analysis software
PIMRider
Protein Interaction Map - Hybrigenics
Pro-3D
Three-Dimensional Protein Analysis Program
RiboClub
Website with RNA related bioingformatic tools
SAM - Sequence Alignment and Modeling System
Flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis.
SeaView
Graphical multiple sequence alignment editor
SeqPup
Biological sequence editor and analysis program
Sequence analysis tools interfaced at the Pasteur Institute
SSAHA2: Sequence Search and Alignment by Hashing Algorithm
Very fast DNA alignment tool
Structural Biology Software Database
TIGR
The Institute for Genome Research
Topali
Open source software developed by Biomathematics & Statistics Scotland (BioSS) for detecting recombination in nucleotide and amino acid sequences. Uses four different algorithms/models. Written in Java.
TraceSearch
Search the whole WTSI trace archive by sequence similarity
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