Use our search function, browse the complete software collection or click on one of the software categories listed below:
Genetic Analysis: GWAS Genetic Variation Linkage Analysis Gene Expression
Sequence Analysis: Assembly Annotation Alignment RNAi RNA-seq Primer Design Next Generation Tools Phylogenetic Analysis Gene Structure Viral
MAGENTA is a program that tests whether predefined biological processes or gene sets are enriched for genes associated with a complex disease or trait.
MapMaker is a package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.
MEDEA is a suite of Adobe® Flash® based comparative genomic visualization tools including a Circular Genome Viewer, parallel Genome Map, Synteny Map, and Dot Plot.
A collection of recent publications aimed at identifying the drivers of medulloblastoma, such as mutations or chromosome alterations, which will enable development of more effective and and less toxic targeted therapies.
Mirador is an open-source tool for visual exploration of complex datasets, enabling users to discover correlation patterns and derive new hypotheses from the data. Mirador's main interface allows to examine scatter, histogram, and eikosogram plots between any pair of variables in the dataset, and to dynamically adjust controlling factors or covariates. Variables can be ranked by their correlation score (based on Mutual Information) with a particular variable of interest, in order to find the most significant explanatory factors for a dependent variable under study. Data can be exported for further analysis with other tools.
The Multiple Myeloma Genomics Portal (MMGP) provides access to and analysis of the MMGP portal data sets. These include the MMRC-funded reference collection of paired aCGH and gene expression data as well as several additional public multiple myeloma datasets.
The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences.
NMF (Non-negative Matrix Factorization), an algorithm based on decomposition-by-parts, recovers meaningful information without supervision. Coupled with a novel model selection mechanism, and efficiently implemented in Matlab, NMF is a powerful method for identification of context-dependent patterns in complex biological systems.
Please cite our Bioinformatics paper if you are using Nozzle in your work.
Pilon uses read alignment analysis to diagnose, report, and automatically improve genome assemblies, and it can also be used to make variant calls among similar haploid strains.