Bioinformatics Doi

USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations. USeq is under continuous development at... Platforms: Windows

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and... Platforms: Mac

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and... Platforms: Linux

A fast, efficient search tool for scientists, medical professionals and students who rely on the ability to quickly access the millions of research papers indexed in PubMed. By combining a simple, efficient user interface with fast access to the PubMed database, PubSearch lets you concentrate on... Platforms: Mac

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The... Platforms: Windows

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The... Platforms: Mac

The package generates a feature table from a batch of LC/MS spectra in .cdf format. Instructions: http://www.sph.emory.edu/apLCMS/ References Bioinformatics. 25(15):1930-36. BMC Bioinformatics. 11:559. Platforms: Windows, Mac, BSD

CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms. An overview of the CisPlusFinder can be found in the flowchart.tif file and is described in the following publication: Pierstorff, N., C.M. Bergman &... Platforms: Mac, BSD

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74 Platforms: Windows, Mac, BSD, Linux

Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765 Platforms: Mac, Linux

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component... Platforms: *nix

An R package that performs forward-backward fragment assembling segmentation. Reference: BMC Bioinformatics. 2007 May 3;8:145. Platforms: Windows, Mac, Linux

Feating constructs a classification ensemble comprising a set of local models. It is effective at reducing the error of both stable and unstable learners, including SVM. For details see the paper at http://dx.doi.org/10.1007/s10994-010-5224-5. Platforms: Windows, Mac, Linux

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Platforms: Windows, Mac, Linux

This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. 'Novel computational methods for increasing PCR primer design effectiveness in directed sequencing'. BMC Bioinformatics 2008, 9:191. Platforms: Windows, Mac, Linux

meBiblio is a bibliografic tool to keep the pace with the growing number of articles and references of literature you gather. What does meBiblio do? - Let's you store informations about scientific articles - Helps you storing in a safe place, the PDF (or other) file of the article. - Helps you... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building. Platforms: Windows, Mac, Linux

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java. Platforms: Windows, Mac, Linux

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. * Ready-to-use... Platforms: Windows, Mac, *nix, C/C++, BSD

PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109. Platforms: Mac