Genomes

Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes.

Strudel is a graphical utility designed to help you visualize genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic...

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

AA seriesA ofA programsA designedA forA accurateA andA highA speedA alignmentA ofA shortA readsA toA referenceA genomes.A NovelA featuresA includeA theA useA ofA baseA qualitiesA inA theA readsA andA ambiguousA nucleotideA codesA inA theA referenceA sequencesA forA alignment. KeyA features: -...


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

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.


Platforms: Windows, Mac, Linux

BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.


Platforms: Mac

DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.


Platforms: Windows, Mac, 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

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

A novel algorithm to layout the contigs with more than one reference genomes at a time using global searches


Platforms: Windows, Mac, BSD, Linux

A computational tool to discover location of promoter consensus sequences in bacterial genomes.


Platforms: Windows, Mac, Linux

Syntainia is an innovative tool for visualization of multiple genomes. It presents a simple and intuitive user interface to view and manipulate relationships between groups of genes. With a clearer gene visualization, it is easier for the researcher to identify synteny conservation among multiple...


Platforms: Mac

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project


Platforms: Mac

The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.


Platforms: Windows, Mac, Linux

OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.


Platforms: Windows, Mac, *nix, Flash, BSD Solaris

The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes. This free and open source standalone Java 1.4 application provides: * Display of sequence and annotation tracks (from FASTA, Genbank, GFF, BLAST, BED, Wiggle (WIG), and...


Platforms: Mac

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of...


Platforms: Mac

OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example...


Platforms: Mac

The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the...


Platforms: Mac