Genomic

IMAS is a Visual Analytics system for the discovery of knowledge in genomic information. IMAS enables genomic scientists to rapidly analyze and visualize a set of microbial genomic sequences using tools such as Glimmer, Blast, Clustal-W, Primer3. Platforms: Windows, Mac

Genomic signature using Chaos game representation of frequencies. The zip file includes two examples of genomic signature (A. fulgidus).References:[1] P.J. Deschavanne, A. Giron, J. Vilain, G. Fagot, and B. Fertil. Genomic Signature: Characterization and Classification of Species Assessed by... Platforms: Matlab

ProtAnnot is a small, Java based application is a protein annotation viewer that displays protein annotations in the context of the genomic sequence. This software is a making it easy to see how alternative mRNA structures affect the various protein products encoded at a locus. for WindowsAll Platforms: Windows

TableView is a small, simple application specially designed to help you with the visualization of genomic data. TableView can present data in spreadsheet format, which lets you sort, copy and paste rows, etc. It also lets you view scatter plots comparing columns in the spreadsheet. And when... Platforms: Windows

Gitools, is a framework for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Gitools allows to import data directly from IntOGen and Biomart. Platforms: Windows

GNomEx is Genomic LIMS and Analysis Project Center designed by the Huntsman Cancer Institute for use by microarray and next generation sequencing core facilities and large research laboratories. KWs: Illumina, Affymetrix, Agilent, MAGE, MySQL/Flex... Platforms: Windows

Genovar is a stand-alone software built using the Java programming language in order to detect unknown genomic variants. The program can also analyze SNP-related copy number variant regions, and comprehensively visualize genomic data such as array CGH and sequence alignments results. Platforms: Windows

This project is a collection of applications and approaches to facilitate phylogenomic (phylogenetic and genomic) analytics. Platforms: Mac

Open up the power of 3D environments to researchers working with genomic information. Visualizing large amount of information at disparate locations in the genome while using a vast variety of algoritms makes Sockeye the number one tool for scientists working on genomic data. 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

LocusView is a program for generating images of chromosomal regions annotated with genomic features, experimental data and analysis results. Platforms: Mac

The genomedata package offers tools for accessing large amounts of genomic data. #md5=c6e16624575ec34490c6234e84a993f6 #md5=03265ed43fcf8983a6caa4cb50f2d4cd Platforms: *nix

An automatically-updating library of genomic and genetic data; that provides a fully integrated, visually-advanced toolset for - Sequence alignment and phylogenetics - Sequence analysis, Contig assembly, - primers, restriction analysis - BLAST. Protein structure viewing, NCBI, UniProt, Pubmed... Platforms: Mac

Easyfig enables the creation of linear comparison figures showing BLAST matches between multiple genomic loci or prokaryote genomes. Easyfig has an easy-to-use graphical user interface and is able to launch BLAST searches interactively. Features: BLAST comparisons between multiple genomic regions... Platforms: Windows

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks. Platforms: Windows, Mac, Linux

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms. Platforms: Windows, Mac, Linux

Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based web interface is also available. Please cite: Lee, W., Chen S.L. BioTechniques 33:1334-1341 (Dec 20 Platforms: Windows, Mac, Linux

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or... Platforms: Windows, Mac, Linux

Modware is an easy to use Perl library for querying and modifying genomic data in a Chado database. It provides a powerful link between BioPerl and Chado. This Chado API provides an intutitive way to use Chado from Perl. Platforms: Windows, Mac, Linux

openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database Platforms: Windows, Mac, Linux