Genome

iMethy is a handy, easy to use genome-wide DNA methylation analysis and visualization application based on next generation sequencing. Firstly, it holds the command-line pipeline to align the bisulfite-treated short read, identify the methylcytosine at CG/CHG/CHH sites, detect the methylation...

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is written in Java, and is available for UNIX, Macintosh and...

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.


Platforms: Windows, Mac, Linux

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74


Platforms: Windows, Mac, BSD, Linux

An open-sourced distributed computing client for exploring the results of the Human Genome Project.


Platforms: Windows, Mac, BSD, Linux

GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.


Platforms: Windows, Mac, Linux

The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.


Platforms: Windows, Mac, Linux

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or...


Platforms: Windows, Mac, Linux

The project is for developing libraries for visualizing biological sequence data on the web. The libraries are written in C and currently use a language (lex/yacc) based front end for presenting features on genomes, contigs, or any type of sequence.


Platforms: Mac, BSD, Linux

MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic


Platforms: Windows, Mac, Linux

The Multi-purpose Automated Genome Project Investigation Environment (MAGPIE, http://magpie.ucalgary.ca/), is a software package for the automated curation and presentation of DNA and protein sequences. Freely available under terms of Apache license v2.0


Platforms: Mac, Solaris, Linux

Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.


Platforms: Windows, Mac, Linux

A computational tool to design and annotate metabolic pathways from genome annotations


Platforms: Windows, Mac, Linux

MyGCAT: My Genome Collection With Assigned Taxonomy provides for the management of extremely large sequence databases and allows for the creation of taxon specific BLAST databases. Primariliy a set of PERL scripts and a HTML interface to a MySQL database


Platforms: Windows, Mac, Linux

PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to...


Platforms: Mac, Linux

PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org.


Platforms: Windows, Mac, Linux

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.


Platforms: Mac, Solaris, Linux

SeqGenome Browser, a mini cross-platform local genome browser, was designed for visualizing next-generation sequencing data. It is light, fast and easy to use.


Platforms: Windows, Mac, Linux

SimBac is a software package for simulating bacterial genome evolution. It outputs samples of DNA sequences at each generation & allows testing of major evolutionary mechanisms, including mutation, recombination, genetic drift, and natural selection.


Platforms: Windows, Mac, Linux

SnipPeep is an interactive graphic interface to visualise results from whole genome genotyping. It allows one to visualise single subjects and groups of subjects, and provides a direct connection with the UCSC Genome Browser.


Platforms: Mac