Genome Characterization

RetroMap is a little app designed to assist you in the analysis of LTR retroelements. It is not particularly great for comprehensive identification of elements found in highly nested contexts. Only the most internal element of those which are nested is likely to be identified as a complete...

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.

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence...


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

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

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

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data. Genome Workbench can display sequence data in many ways,...


Platforms: Mac

jContigSort is is an useful Java-based instrument that was designed in order to help you sort genome contigs. Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user.


Platforms: Windows

The Genome Positioning System (GPS) is a software tool to study protein-DNA interaction using ChIP-Seq data. GPS builds a probabilistic mixture model to predict the most likely positions of binding events at single-base resolution. GPS is a Java software, so it runs on multiple platforms,...


Platforms: Windows

GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard...


Platforms: Windows

UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module. for WindowsAll


Platforms: Windows

inGAP is a handy, easy to use application specially designed to offer you an integrative next-generation genome analysis pipeline, which employed a Bayesian principle to detect single nucleotide polymorphisms (SNPs), small insertion/deletions (indels). inGAP has been applied to a number of genome...


Platforms: Windows

tagcna was specially designed using R in order to identify significant consensus events from copy number alterations in cancer genome. Now you can easily identify the events that interest you with the help of this handy and accessible tool.


Platforms: Windows

TB antibiotic resistance mapper was developed as a specialized tool that can help you map sequencing reads with the MTB reference genome (H37Rv) using NCBI blast, in order to find out mutation sites. Now you can quickly discover mutations with the help of this instrument.


Platforms: Windows

Gendraw was specially developed to aid you in drawing genome graphs. It has multiple graphic elements to represent different types of contents. The contents for drawing can be imported from a standard Genbank or EMBL flatfile, or manually given by the user.


Platforms: Windows

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Platforms: Mac

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

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

This script uses the gene name field(s) in a table downloaded from the UCSC Genome Browser to add gene names to an existing SVS marker map saved in the DSM file format. Note: Though the following instructions specify downloading a table containing genes based on the Mar. 2006 (NCBI36/hg18) Human...


Platforms: Mac

miRpp - A Plant microRNA Precursor Prediction Tool for Small RNA Reads on Genome Sequences


Platforms: Mac