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...

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 -...

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

This toolbox provides direct access to cancer genomics data from within the MATLAB environment. The toolbox will query the Cancer Genomics Data Server Web API, provided by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center, and return data in a structured format.A tutorial...


Platforms: Matlab

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

QSB is a computational tool developed for genetical genomics, an emerging field that combines quantitative genetics and genomics. QSB takes marker genotype data and expression microarray data of a segregating population as input and identify the significant QTLs that module gene expression. DNA...


Platforms: Mac

Image analysis and data inspection for agar plates generated in high-throughput yeast genetics and genomics experiments.


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

Performs Mantel-Haenszel's test for k strata of 2x2 tables.Mantel and Haenszel proposed this asymptotic test based on the chi-2 distribution. Assuming no three-way interaction (k independent strata). Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Input: X: data matrix...


Platforms: Matlab

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


Platforms: Matlab

Chi-square tests of homogeneity and independence.Computes the P-value for I x J - table row/col independence.Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Input:X: data matrix (I x J -table) of the observed frequency cells.method: 'RC': Read-Cressie power divergence...


Platforms: Matlab

It is a non-parametric statistical test for discrete data used todetermine if there are nonrandom associations between the two variables.Mid-P values are a reasonable compromise between the conservativeness ofthe ordinary exact test and the uncertain adequacy of large-sample methods.Mid-P values...


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