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
ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads.
AmosCmp16Spipeline uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene.
Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.
The Argo Genome Browser is a production tool for visualizing and manually annotating whole genomes.
ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
ComSeq is a tool for designing and analyzing combinatorial pooling experiments for next-generation sequencing projects using compressed sensing technology. ComSeq enables the identification of novel rare alleles, as well as detection of individuals who are carriers of known SNPs in a large population in an efficient manner.
GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. It includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, GENE-E also contains tools that are designed specifically for RNAi and gene expression data.
GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. GenomeSpace does not perform any analyses itself; these are done within the member tools wherever they live – desktop, Web service, cloud, in-house server, etc. Rather, GenomeSpace provides tool selection and launch capabilities, and acts as a data highway automatically reformatting data as required when results move from the output of one tool to input for the next.
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules are available to evaluate the completeness of the kinome and place it in context with reference kinomes.
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.