Biology

biOpen biOpen- Commercial Mac OS X sequence analysis and structure visualization software. BioMAJ BioMAJ- Workflow engine dedicated to bio-data synchronization and processing. Geneious Geneious- This research software is designed for biologists and not computer scientists. It combines all the major DNA and protein sequence analysis tools into one software soluti… MARBL MARBL- MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH. BioEdit BioEdit- Free Windows biological sequence alignment editor. FASTA FASTA- William Pearson's package for fast sequence comparison tools. PhyloSort PhyloSort- A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units. DNPTrapper DNPTrapper- A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. Genome-tools Web Interface Genome-tools Web Interface- Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. SeWeR SeWeR- An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application. Gints Gints- Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English. Seqtools Seqtools- Commercial Windows software for batch handling and analysis of nucleotide and protein sequences. Sockeye Sockeye- 3D visualisation platform for Comparative Genomics visualisation. ADF MAGE-ML ADF MAGE-ML- Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML). INCA - INteractive Codon Analysis INCA - INteractive Codon Analysis- Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the … Tandem Repeats Finder Tandem Repeats Finder- Locates and displays tandem repeats in DNA sequences. MIRA MIRA- A sequence assembly suite with SNP detection for "hard" projects. RGBG Analyzer RGBG Analyzer- Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 and XP. DNAMAN DNAMAN- Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X. Genespotter Genespotter- Commercial Windows software for analyzing biochip image data. MedScan MedScan- Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature. MaGe (Magnifying Genomes) - Microbial genome Annotation System MaGe (Magnifying Genomes) - Microbial genome Annotation System- The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of… EMBOSS EMBOSS- The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG. JAligner JAligner- Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. limmaGUI limmaGUI- A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes. ARCiB -- Accessible Retired Computers in Biology ARCiB -- Accessible Retired Computers in Biology- NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental … AnnHyb AnnHyb- Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrie… The ARB Project The ARB Project- A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and g… Sequence Analysis Sequence Analysis- A freeware Java application that does many standard types of DNA and protein sequence analysis tasks. pDRAW32 pDRAW32- Freeware DNA cloning, analysis and visualization software. Darwin Darwin- An interactive tool for peptide and nucleotide sequence analysis. Phrap/Consed Phrap/Consed- DNA sequence assembler and finishing tools from the UW Genome Center. Premier Biosoft International Premier Biosoft International- Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, p… XDigitize XDigitize- A Linux/Unix visualization software system for evaluation of hybridisation experiments. Icahn School of Medicine at Mount Sinai: Bioinformatics Laboratory Icahn School of Medicine at Mount Sinai: Bioinformatics Laboratory- Provides an overview of the laboratory and details of publications, research projects and the research team. Helix Group at Stanford Helix Group at Stanford- This is a research group within the Stanford Medical Informatics laboratory directed by Russ Altman, MD, PhD. They focus on the application of computation… South African National Bioinformatics Institute South African National Bioinformatics Institute- SANBI aims to bring genome information, computational biology, and analytical tools to the South African research community. Overv… Purdue University: Kihara Bioinformatics Laboratory Purdue University: Kihara Bioinformatics Laboratory- Provides information on the areas of research, projects, people and publications. St. Petersburg State Polytechnical University: Department of Computational Biology St. Petersburg State Polytechnical University: Department of Computational Biology- General departmental information, publications, awards and staff. Also include an overview of t… Research Institute of Molecular Pathology: IMBA Bioinformatics Group Research Institute of Molecular Pathology: IMBA Bioinformatics Group- Offers inter-disciplinary expertise in biocomputing and information technology including sequence analysis an… BioAfrica BioAfrica- Rural research center in South Africa funded by the Wellcome Trust providing bioinformatics research and software. GeoPense GeoPense- Worldwide volunteer computing teams harnessing institutional and individual resources to contribute to basic science research. Early projects include protein folding and… Linnaeus Centre for Bioinformatics Linnaeus Centre for Bioinformatics- At Uppsala, Sweden. Research areas include algorithms and databases, genome studies, expression and function, and structure and design. Runs co… UC Santa Cruz: Bioinformatics, Applied Mathematics and Biostatistics UC Santa Cruz: Bioinformatics, Applied Mathematics and Biostatistics- Interests include assembling the human genome, protein structure prediction, stochastic context-free grammars… Dinulab Dinulab- Provides information on research, led by Dr Valentin Dinu at Arizona State University, into the assessment, improvement and development of computational approaches, softw… Supercomputing Facility for Bioinformatics and Computational Biology Supercomputing Facility for Bioinformatics and Computational Biology- This facility at the Indian Institute of Technology aims to establish a nodal facility for supercomputing and… Center Systems Biology: University of Stuttgart Center Systems Biology: University of Stuttgart- Provides details of the Center, research, seminars, the central imaging project, partnerships, events and links. Computational Biology and Bioinformatics Computational Biology and Bioinformatics- Group at Charité Berlin developing algorithms and applications in the field of gene ontology, phenotypic analysis, machine learning and m… Wold Lab: Bioinformatics Wold Lab: Bioinformatics- The Wold Lab at the California Institute of Technology is interested in the composition, evolution and function of regulatory networks that govern how ma… Bioinformatics Computational Core Laboratories Bioinformatics Computational Core Laboratories- Research at BCCL at Virginia Commonwealth University is focused on the Cryptosporidium hominis genome sequencing project.