BioSoftwares

A-MADMAN is an open source web application and gene chip analysis automation framework for annotation-based meta-analysis of data from public repositories (NCBI GEO).

Comparative genomics study the evolution of gene organization, which in the past years was by the fast growing number of full genome sequences available in public repositories. Most of the available bioinformatics tools for visualization and comparison of genomes are restricted to two or three genomes at a time, which is a significant limitation in the field of comparative genomics. Recently (this month) a new phylogenetic software was announced – Genomicus. It provides functionality of a synteny browser, which can represent and compare unlimited numbers of genomes in a broad phylogenetic view. The tool provides reconstructed ancestral gene organization, in a way that facilitates the interpretation of the analysis data.

BioEdit is a mouse-driven, easy-to-use sequence alignment editor and sequence analysis program designed and written by a graduate student who knows how frustrating and time consuming it can be to rely upon word-processors and command-line programs for sequence manipulation

NoteExpress is a perfect assistant and information manager for researchers, scholars, students, and librarians. NoteExpress is designed to help you organize research notes and bibliographic references, generate bibliographies automatically, search and capture bibliographic data from Internet with efficiency and ease

The FastPCR software is an integrated tools environment that provides comprehensive facilities for designing any kind of PCR primers for standard, long distance, inverse, real-time PCR (LUX and self-reporting), multiplex PCR, group-specific PCR (common primers for given N target sequences), unique PCR (design of specific (unique) PCR primers for each sequence); single primer PCR (design of PCR primers from close located inverted repeat), automatically detecting SSR loci and direct PCR primer design, amino acid sequence degenerate PCR and more. The software consists of a data editor; build-in commands for probe/primers design and build automation tools

The Microarray Explorer (MAExplorer) is a Java-based data-mining facility for microarray databases. It may be freely downloaded and run as a stand-alone application on your computer. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays

Gathering and managing data from diverse and heterogeneous datasets is central to many systems approaches to biology. Systems biologists need to easily identify and gather the information they require and then integrate and analysis the experimental and reference data sets which can come from myriad databases with a wide variety of formats and access methods. Continue reading →

Avogadro is a new, open source molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc

Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data.