Genomics

Microbial Genomics Tool or, MGT, for short is a Graphical User Interface instrument that can run on multiple platforms. The main goal of the program is to provide a useful and comprehensive codon analysis via an interactive environment, which can be started up and used easily with as little... Platforms: Windows

Using super-fast, integrated, high-performance computing algorithms, CLC Genomics Workbench sets a new standard for desktop based reference assembly and de novo assembly of SOLiD, Solexa, 454, and Helicos sequencing data# De novo assembly of Sanger, 454, Solexa, Helicos, and SOLiD data -... Platforms: Mac

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV Platforms: Windows, Mac, Linux

An award winning, integrated on-line learning environment where users experience the world of biology through discovery-based learning. GDL was developed as a series of curriculum-aligned and integrated games, modules, and interactive simulations covering an array of topics in biology. To meet... Platforms: Mac

The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006. Platforms: Linux

PGDSpider was built using the Java programming language as a conversion app for population genetics and genomics programs. The software facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic... Platforms: Windows

The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006. Platforms: Linux

GenomePixelizer is a program for comparative genomics, detection of duplication events in genomes, tracking the 'footprints' of evolution. It may be considered as a drawing tool that generates custom images of genomes out of the given set of genes. Platforms: Windows, Mac, BSD, Linux

GenoViz provides software applications and re-usable components for genomics data visualization and data sharing. One included project is IGB: the Integrated Genome Browser. Documentation is available from http://sourceforge.net/apps/trac/genoviz/ Platforms: Windows, Mac, BSD, Linux

The MIPE (Minimal Information for PCR Experiments) format is a XML format that enables genomics researchers to store critical information on PCR experiments.Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file. Platforms: Windows, Mac, Linux

pygr is a bioinformatics toolkit for sequence analysis and comparative genomics. pygr is highly scalable (e.g. one can easily query multi-genome alignments) and easy to use. Please see our new project page and wiki at http://code.google.com/p/pygr. Platforms: Windows, Mac, Linux

DISOPE + MOMENTUM + PARTAN Algorithm to improve convergence of a nonlinear dynamic system.Study covers application for chemical process industries, robotics, genomics, etc. Platforms: Matlab

A powerful and user-friendly graphical software designed to conduct large scale exploration of biological sequence databanks and related information (functional, taxonomy, pathways, mutations, etc). KoriBlast can be used for a wide range of applications in genomics and proteomics, such as: full... Platforms: Mac

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and... Platforms: Mac, Java 1.5 or later

PriorsEditor is a general workbench for regulatory region analysis and transcription factor binding site discovery. The program emphasizes the use of positional priors to focus the search for binding sites towards portions of DNA sequences that are considered more likely to contain true... Platforms: Mac

bedtools: a flexible suite of utilities for comparing genomic features. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.... Platforms: Mac